diff --git a/DESCRIPTION b/DESCRIPTION index 29593462..83ae821f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: netZooR Type: Package Title: Unified methods for the inference and analysis of gene regulatory networks -Version: 1.1.15 +Version: 1.1.16 Date: 2022-07-07 Authors@R: c(person("Marouen", "Ben Guebila", email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")), diff --git a/NAMESPACE b/NAMESPACE index b73dc999..29f527a0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -31,6 +31,7 @@ export(monsterTransitionNetworkPlot) export(monsterTransitionPCAPlot) export(monsterdTFIPlot) export(otter) +export(pandaDiffEdges) export(pandaPy) export(pandaToAlpaca) export(pandaToCondorObject) diff --git a/R/PANDA.R b/R/PANDA.R index 40f9c3f3..976a32fe 100644 --- a/R/PANDA.R +++ b/R/PANDA.R @@ -65,7 +65,7 @@ #' -pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", precision="double",save_memory=FALSE, save_tmp=TRUE, keep_expression_matrix=FALSE, modeProcess="union", remove_missing=FALSE){ +pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", precision="double",save_memory=FALSE, save_tmp=TRUE, keep_expression_matrix=FALSE, modeProcess="union", remove_missing=FALSE, with_header=FALSE){ if(missing(expr_file)){ stop("Please provide the path of gene expression data file to 'expr_file' variable") } @@ -106,6 +106,13 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", keepexpression.str <- "keep_expression_matrix=True" } else{ keepexpression.str <- "keep_expression_matrix=False" } + # with header option + if(with_header==FALSE){ + withheader.str <- "with_header=False" + }else if (with_header==TRUE){ + withheader.str <- "with_header=True" + } + # when pre-processing mode is legacy if(modeProcess == "legacy"){ @@ -130,7 +137,9 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu", reticulate::source_python(pandapath,convert = TRUE) # invoke Python script to create a Panda object - obj.str <- paste("panda_obj=Panda(", expr.str, ",", motif.str,",", ppi.str, ",", computing.str, ",", precision.str, ",", savememory.str, ",", savetmp.str, "," , keepexpression.str, ",", mode.str, ")", sep ='') + obj.str <- paste("panda_obj=Panda(", expr.str, ",", motif.str,",", ppi.str, ",", + computing.str, ",", precision.str, ",", savememory.str, ",", savetmp.str, "," , + keepexpression.str, ",", mode.str, "," , withheader.str, ")", sep ='') # run Python code py_run_string(obj.str) diff --git a/docs/404.html b/docs/404.html index 40cee443..8ddfd96c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ netZooR - 1.0.4 + 1.1.16 @@ -130,6 +130,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization + +
  • + Changelog
    • + +
  • + Changelog
    • + +
  • + Changelog
    • + +
  • + Changelog
    • + +
  • + Changelog
    • + +
  • + Changelog
    • + +
  • + Changelog
      • @@ -147,7 +150,7 @@

      Workflow

      -library(netZooR)
      +library(netZooR)

      condor works with an edgelist (elist in the code below) as its input.

       r = c(1,1,1,2,2,2,3,3,3,4,4);
@@ -168,30 +171,30 @@ 
      
 condor.object <- condorCluster(condor.object)
      ## [1] "modularity of projected graph 0"
 ## [1] "Q = 0"
-## [1] "Q = 0.198347107438017"
-## [1] "Q = 0.231404958677686"
-## [1] "Q = 0.231404958677686"
      +## [1] "Q = 0.132231404958678" +## [1] "Q = 0.148760330578512" +## [1] "Q = 0.148760330578512"       
       print(condor.object$red.memb)
      ##   red.names com
 ## 1     Alice   1
-## 2    Janine   2
-## 3      Mary   2
-## 4       Sue   1
      +## 2 Janine 1 +## 3 Mary 1 +## 4 Sue 2       
       print(condor.object$blue.memb)
      ##   blue.names com
-## 1        Bob   1
-## 2         Ed   2
+## 1        Bob   2
+## 2         Ed   1
 ## 3       Hank   2
-## 4       John   1
      +## 4 John 2

      Nodes in first community are {Alice, John, Bob, Sue}, nodes in second community are {Ed, Janine, Hank, Mary} based on the modularity maximization. Here’s a picture:

       gtoy = graph.edgelist(as.matrix(elist),directed=FALSE)
 set.graph.attribute(gtoy, "layout", layout.kamada.kawai(gtoy))
      -
      ## IGRAPH 694fdca UN-- 8 11 -- 
+
      ## IGRAPH d53f3f0 UN-- 8 11 -- 
 ## + attr: layout (g/n), name (v/c)
-## + edges from 694fdca (vertex names):
+## + edges from d53f3f0 (vertex names):
 ##  [1] Alice--Bob    Alice--John   Alice--Ed     Bob  --Sue    John --Sue   
 ##  [6] Sue  --Hank   John --Janine Ed   --Janine Hank --Janine Ed   --Mary  
 ## [11] Hank --Mary
      
@@ -242,7 +245,7 @@ 
      
 ## [8] base     
 ## 
 ## other attached packages:
-## [1] netZooR_1.0.4       yarn_1.18.0         pandaR_1.19.5      
+## [1] netZooR_1.1.16      yarn_1.18.0         pandaR_1.19.5      
 ## [4] Biobase_2.52.0      BiocGenerics_0.38.0 reticulate_1.22    
 ## [7] igraph_1.2.6       
 ## 
@@ -356,7 +359,7 @@ 
      
 
 
       
      
-  
      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.
      
+  
      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.
      
 
      
 
 
      
diff --git a/docs/articles/CONDOR_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/CONDOR_files/figure-html/unnamed-chunk-10-1.png
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diff --git a/docs/articles/EGRET_toy_example.html b/docs/articles/EGRET_toy_example.html
index 84141aaa..1ec64d2e 100644
--- a/docs/articles/EGRET_toy_example.html
+++ b/docs/articles/EGRET_toy_example.html
@@ -31,7 +31,7 @@
       
       
         netZooR
-        1.0.4
+        1.1.16
       
     
      
 
@@ -90,6 +90,9 @@
       YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization
    + +
  • + Changelog
      • @@ -143,7 +146,7 @@

      #devtools::install_github("netZoo/netZooR@devel")

      Load the netZooR package:

      -library(netZooR)
      +library(netZooR)

      @@ -416,7 +419,7 @@

      -

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

      +

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

      diff --git a/docs/articles/LionessApplicationinGTExData.html b/docs/articles/LionessApplicationinGTExData.html index 95f914a0..2e4c760b 100644 --- a/docs/articles/LionessApplicationinGTExData.html +++ b/docs/articles/LionessApplicationinGTExData.html @@ -31,7 +31,7 @@ netZooR - 1.0.4 + 1.1.16
      @@ -90,6 +90,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

    + +
  • + Changelog
      • @@ -328,20 +331,20 @@

      pathways <- gmtPathways("./c2.cp.kegg.v7.0.symbols.gmt") fgseaRes <- fgsea(pathways, indegree_rank, minSize=15, maxSize=500, nperm=1000) head(fgseaRes) -#> pathway pval padj ES -#> 1: KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.12400000 0.2292558 0.3240518 -#> 2: KEGG_CITRATE_CYCLE_TCA_CYCLE 0.56024096 0.6973246 -0.2702159 -#> 3: KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.22200393 0.3529862 0.3795079 -#> 4: KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.04715128 0.1086529 0.4200039 -#> 5: KEGG_GALACTOSE_METABOLISM 0.85887097 0.9289829 -0.2250237 -#> 6: KEGG_FATTY_ACID_METABOLISM 0.14421252 0.2576381 0.3533304 +#> pathway pval padj ES +#> 1: KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.1187384 0.2145387 0.3240518 +#> 2: KEGG_CITRATE_CYCLE_TCA_CYCLE 0.5534591 0.6929134 -0.2702159 +#> 3: KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.2008032 0.3192771 0.3795079 +#> 4: KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.0458891 0.1027657 0.4200039 +#> 5: KEGG_GALACTOSE_METABOLISM 0.8804781 0.9567555 -0.2250237 +#> 6: KEGG_FATTY_ACID_METABOLISM 0.1349810 0.2358459 0.3533304 #> NES nMoreExtreme size leadingEdge -#> 1: 1.2651079 61 47 ALDOB,TPI1,ALDH3A1,BPGM,PKLR,PDHB,... -#> 2: -0.9429714 278 29 SDHA,CS,OGDH,PDHA1,ACO2,OGDHL,... -#> 3: 1.2043744 112 21 ALDOB,DERA,RPE,TALDO1,PGM2,ALDOC,... -#> 4: 1.4597462 23 30 ALDOB,TSTA3,MTMR6,TPI1,FPGT,PMM2,... -#> 5: -0.7079013 425 20 HK1,GLA,GANC,PFKL,UGP2,PFKM -#> 6: 1.2642168 75 33 GCDH,ACAT2,ACOX3,EHHADH,ECHS1,CPT2,... +#> 1: 1.2593265 63 47 ALDOB,TPI1,ALDH3A1,BPGM,PKLR,PDHB,... +#> 2: -0.9513020 263 29 SDHA,CS,OGDH,PDHA1,ACO2,OGDHL,... +#> 3: 1.2181659 99 21 ALDOB,DERA,RPE,TALDO1,PGM2,ALDOC,... +#> 4: 1.4556415 23 30 ALDOB,TSTA3,MTMR6,TPI1,FPGT,PMM2,... +#> 5: -0.7229038 441 20 HK1,GLA,GANC,PFKL,UGP2,PFKM +#> 6: 1.2581352 70 33 GCDH,ACAT2,ACOX3,EHHADH,ECHS1,CPT2,... # Subset to pathways with FDR < 0.05 sig <- fgseaRes[fgseaRes$padj < 0.05,] # Top 10 pathways enriched in females @@ -355,7 +358,7 @@

      #> [7] "KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450" #> [8] "KEGG_DRUG_METABOLISM_CYTOCHROME_P450" #> [9] "KEGG_RIBOSOME" -#> [10] "KEGG_PROTEASOME" +#> [10] "KEGG_DNA_REPLICATION" # Top 10 pathways enriched in males sig$pathway[sig$NES < 0][1:10] #> [1] "KEGG_INOSITOL_PHOSPHATE_METABOLISM" @@ -430,7 +433,7 @@

      -

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

      +

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

      diff --git a/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-6-1.png index 2df33dd6..ead6d27f 100644 Binary files a/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-9-1.png index c4c79e58..7209d23e 100644 Binary files a/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-9-1.png and b/docs/articles/LionessApplicationinGTExData_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/docs/articles/MONSTER.html b/docs/articles/MONSTER.html index d56401e3..190f46d9 100644 --- a/docs/articles/MONSTER.html +++ b/docs/articles/MONSTER.html @@ -31,7 +31,7 @@ netZooR - 1.0.4 + 1.1.16
      @@ -90,6 +90,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

    + +
  • + Changelog
      • @@ -140,7 +143,7 @@

      # install netZooR pkg with vignettes, otherwise remove the "build_vignettes = TRUE" argument. devtools::install_github("netZoo/netZooR", build_vignettes = TRUE) 
      -library(netZooR)
      +library(netZooR)

      @@ -203,12 +206,12 @@

      #> [1] "Running iteration 1" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 6.29425e-05 secs +#> Time difference of 6.008148e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.605553e-05 secs +#> Time difference of 9.10759e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -216,12 +219,12 @@

      #> [1] "Running iteration 2" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.796288e-05 secs +#> Time difference of 8.201599e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.201599e-05 secs +#> Time difference of 9.584427e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -229,12 +232,12 @@

      #> [1] "Running iteration 3" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.605553e-05 secs +#> Time difference of 8.511543e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.106232e-05 secs +#> Time difference of 7.390976e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -242,12 +245,12 @@

      #> [1] "Running iteration 4" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.414818e-05 secs +#> Time difference of 7.796288e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.104874e-05 secs +#> Time difference of 7.796288e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -255,12 +258,12 @@

      #> [1] "Running iteration 5" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.296967e-05 secs +#> Time difference of 8.416176e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.104874e-05 secs +#> Time difference of 8.487701e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -268,12 +271,12 @@

      #> [1] "Running iteration 6" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.915497e-05 secs +#> Time difference of 7.486343e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.605553e-05 secs +#> Time difference of 8.106232e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -281,27 +284,25 @@

      #> [1] "Running iteration 7" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.796288e-05 secs +#> Time difference of 8.487701e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.606911e-05 secs +#> Time difference of 8.487701e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" -#> ....................... -#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred -#> ..............................[1] "Using OLS method" +#> .....................................................[1] "Using OLS method" #> [1] "Finished running iteration 7" #> [1] "Running iteration 8" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.392334e-05 secs +#> Time difference of 7.31945e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.392334e-05 secs +#> Time difference of 7.915497e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -309,12 +310,14 @@

      #> [1] "Running iteration 9" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.605553e-05 secs +#> Time difference of 8.106232e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" -#> .....................................................[1] "Initializing and validating" +#> ....................... +#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred +#> ..............................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.31945e-05 secs +#> Time difference of 0.0003321171 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -322,12 +325,12 @@

      #> [1] "Running iteration 10" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 9.012222e-05 secs +#> Time difference of 0.0001831055 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.487701e-05 secs +#> Time difference of 0.0001070499 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -335,25 +338,27 @@

      #> [1] "Running iteration 11" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.820129e-05 secs +#> Time difference of 0.0002679825 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.201599e-05 secs +#> Time difference of 7.987022e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" -#> .....................................................[1] "Using OLS method" +#> ....................... +#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred +#> ..............................[1] "Using OLS method" #> [1] "Finished running iteration 11" #> [1] "Running iteration 12" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.987022e-05 secs +#> Time difference of 8.893013e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.296967e-05 secs +#> Time difference of 8.821487e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -361,12 +366,12 @@

      #> [1] "Running iteration 13" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 7.915497e-05 secs +#> Time difference of 7.009506e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.010864e-05 secs +#> Time difference of 7.414818e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -374,12 +379,12 @@

      #> [1] "Running iteration 14" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.201599e-05 secs +#> Time difference of 7.009506e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.010864e-05 secs +#> Time difference of 7.31945e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -387,12 +392,12 @@

      #> [1] "Running iteration 15" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.106232e-05 secs +#> Time difference of 0.0001008511 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 8.606911e-05 secs +#> Time difference of 0.0001218319 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -400,27 +405,25 @@

      #> [1] "Running iteration 16" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 9.799004e-05 secs +#> Time difference of 7.796288e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 9.083748e-05 secs +#> Time difference of 7.915497e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" -#> ....................... -#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred -#> ..............................[1] "Using OLS method" +#> .....................................................[1] "Using OLS method" #> [1] "Finished running iteration 16" #> [1] "Running iteration 17" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 9.608269e-05 secs +#> Time difference of 9.489059e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 9.608269e-05 secs +#> Time difference of 0.0002009869 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -428,12 +431,12 @@

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      #> Time difference of 0.0001051426 secs #> [1] "More data cleaning" #> [1] "Main calculation" -#> ....................... -#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred -#> ..............................[1] "Using OLS method" +#> .....................................................[1] "Using OLS method" #> [1] "Finished running iteration 80" #> [1] "Running iteration 81" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 9.608269e-05 secs +#> Time difference of 9.703636e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001149178 secs +#> Time difference of 9.608269e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1278,12 +1279,12 @@

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      #> [1] "Running iteration 92" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001010895 secs +#> Time difference of 0.0001029968 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001142025 secs +#> Time difference of 0.0001111031 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1423,12 +1424,12 @@

      #> [1] "Running iteration 93" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001111031 secs +#> Time difference of 0.0001208782 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001120567 secs +#> Time difference of 9.298325e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1436,12 +1437,12 @@

      #> [1] "Running iteration 94" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001199245 secs +#> Time difference of 0.0001001358 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001111031 secs +#> Time difference of 0.0001189709 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1449,12 +1450,12 @@

      #> [1] "Running iteration 95" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001111031 secs +#> Time difference of 9.608269e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001170635 secs +#> Time difference of 9.799004e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1462,12 +1463,12 @@

      #> [1] "Running iteration 96" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001149178 secs +#> Time difference of 9.584427e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001111031 secs +#> Time difference of 9.608269e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1475,12 +1476,12 @@

      #> [1] "Running iteration 97" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001029968 secs +#> Time difference of 0.0001308918 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001060963 secs +#> Time difference of 0.0001080036 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1488,12 +1489,12 @@

      #> [1] "Running iteration 98" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001020432 secs +#> Time difference of 9.703636e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001409054 secs +#> Time difference of 0.0001239777 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1501,12 +1502,12 @@

      #> [1] "Running iteration 99" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001130104 secs +#> Time difference of 0.0001268387 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.000109911 secs +#> Time difference of 0.0001060963 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1514,12 +1515,12 @@

      #> [1] "Running iteration 100" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.000109911 secs +#> Time difference of 9.918213e-05 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001091957 secs +#> Time difference of 0.0001018047 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" @@ -1527,17 +1528,17 @@

      #> [1] "Running iteration 101" #> [1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001158714 secs +#> Time difference of 0.0001211166 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Initializing and validating" #> [1] "Verified adequate samples, calculating correlation matrix" -#> Time difference of 0.0001120567 secs +#> Time difference of 0.0001218319 secs #> [1] "More data cleaning" #> [1] "Main calculation" #> .....................................................[1] "Using OLS method" #> [1] "Finished running iteration 101" -#> Time difference of 5.257792 mins

      +#> Time difference of 4.959143 mins

      We can print the details of the analysis result

       monsterRes
@@ -1621,7 +1622,7 @@ 
      
 
 
       
      
-  
      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.
      
+  
      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.
      
 
      
 
 
      
diff --git a/docs/articles/MONSTER_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/MONSTER_files/figure-html/unnamed-chunk-10-1.png
index 13483032..086c4b44 100644
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diff --git a/docs/articles/MONSTER_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/MONSTER_files/figure-html/unnamed-chunk-11-1.png
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diff --git a/docs/articles/MONSTER_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/MONSTER_files/figure-html/unnamed-chunk-13-1.png
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diff --git a/docs/articles/SAMBAR.html b/docs/articles/SAMBAR.html
index c7b0925b..b63caa0d 100644
--- a/docs/articles/SAMBAR.html
+++ b/docs/articles/SAMBAR.html
@@ -31,7 +31,7 @@
       
       
         netZooR
-        1.0.4
+        1.1.16
       
     
      
 
@@ -90,6 +90,9 @@
       YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

    + +
  • + Changelog
      • @@ -157,7 +160,7 @@

      -

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

      +

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

      diff --git a/docs/articles/TutorialOTTER.html b/docs/articles/TutorialOTTER.html index 60100999..f98373fa 100644 --- a/docs/articles/TutorialOTTER.html +++ b/docs/articles/TutorialOTTER.html @@ -31,7 +31,7 @@ netZooR - 1.0.4 + 1.1.16
      @@ -90,6 +90,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

    + +
  • + Changelog
      • @@ -148,7 +151,7 @@

      Load packages

      -library(netZooR)
+library(netZooR)
 library(fgsea)
 library(ggplot2)
 library(reshape2)
@@ -357,34 +360,34 @@ 
      
 fgseaRes <- fgsea(pathways, degreeDiff_all, minSize=15, maxSize=500, nperm=1000)
 head(fgseaRes)
 #>                                          pathway        pval       padj
-#> 1:               KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.002132196 0.01534327
-#> 2:                  KEGG_CITRATE_CYCLE_TCA_CYCLE 0.248175182 0.40972222
-#> 3:                KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.069387755 0.15950172
-#> 4: KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.433609959 0.61020175
-#> 5:          KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.050772627 0.13024283
-#> 6:                     KEGG_GALACTOSE_METABOLISM 0.347368421 0.52105263
+#> 1:               KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.002028398 0.01741098
+#> 2:                  KEGG_CITRATE_CYCLE_TCA_CYCLE 0.217131474 0.36256859
+#> 3:                KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.083168317 0.17735894
+#> 4: KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.390873016 0.56708626
+#> 5:          KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.036734694 0.10659083
+#> 6:                     KEGG_GALACTOSE_METABOLISM 0.329243354 0.49808610
 #>            ES       NES nMoreExtreme size                          leadingEdge
-#> 1:  0.4360719  1.786218            0   58    HK1,ENO2,ENO1,ALDOC,BPGM,PFKM,...
-#> 2: -0.3428560 -1.153405          135   29  DLST,PCK2,SUCLG2P2,MDH2,FH,IDH2,...
-#> 3:  0.4435710  1.430352           33   21   ALDOC,PFKM,PFKP,ALDOA,PFKL,GPI,...
-#> 4:  0.3180477  1.029746          208   22   UGT1A1,UGT1A10,UGT1A6,CRYL1,UGT2B7
-#> 5:  0.4118882  1.445861           22   31 HK1,ALDOC,PFKFB4,PFKM,MTMR2,PFKP,...
-#> 6:  0.3247973  1.082019          164   25      GLB1,HK1,PFKM,PFKP,PFKL,GAA,...
+#> 1:  0.4360719  1.779675            0   58    HK1,ENO2,ENO1,ALDOC,BPGM,PFKM,...
+#> 2: -0.3428560 -1.172256          108   29  DLST,PCK2,SUCLG2P2,MDH2,FH,IDH2,...
+#> 3:  0.4435710  1.414328           41   21   ALDOC,PFKM,PFKP,ALDOA,PFKL,GPI,...
+#> 4:  0.3180477  1.031980          196   22   UGT1A1,UGT1A10,UGT1A6,CRYL1,UGT2B7
+#> 5:  0.4118882  1.458885           17   31 HK1,ALDOC,PFKFB4,PFKM,MTMR2,PFKP,...
+#> 6:  0.3247973  1.088178          160   25      GLB1,HK1,PFKM,PFKP,PFKL,GAA,...
 # Subset to pathways with FDR < 0.05
 sig <- fgseaRes[fgseaRes$padj < 0.05,]
 # Get the top 10 significant pathways enriched for genes having lower targeting in LCLs  
 sig[order(sig$NES)[1:10],]
 #>                             pathway        pval       padj         ES       NES
-#>  1:            KEGG_DNA_REPLICATION 0.001841621 0.01534327 -0.7725018 -2.724198
-#>  2:                 KEGG_CELL_CYCLE 0.001751313 0.01534327 -0.5948628 -2.683607
-#>  3:                KEGG_SPLICEOSOME 0.001776199 0.01534327 -0.5766563 -2.582334
-#>  4:             KEGG_PROTEIN_EXPORT 0.001897533 0.01534327 -0.6851677 -2.181782
-#>  5: KEGG_NUCLEOTIDE_EXCISION_REPAIR 0.001838235 0.01534327 -0.5785505 -2.114989
-#>  6:       KEGG_BASE_EXCISION_REPAIR 0.001818182 0.01534327 -0.5965607 -2.087925
-#>  7:      KEGG_PYRIMIDINE_METABOLISM 0.001811594 0.01534327 -0.4606911 -1.957338
-#>  8:             KEGG_RNA_POLYMERASE 0.001862197 0.01534327 -0.5731001 -1.906608
-#>  9:            KEGG_MISMATCH_REPAIR 0.005769231 0.03094406 -0.6107380 -1.904153
-#> 10:      KEGG_N_GLYCAN_BIOSYNTHESIS 0.003703704 0.02260536 -0.4815544 -1.793979
+#>  1:            KEGG_DNA_REPLICATION 0.001901141 0.01741098 -0.7725018 -2.758721
+#>  2:                 KEGG_CELL_CYCLE 0.001773050 0.01741098 -0.5948628 -2.744328
+#>  3:                KEGG_SPLICEOSOME 0.001795332 0.01741098 -0.5766563 -2.635589
+#>  4:             KEGG_PROTEIN_EXPORT 0.001980198 0.01741098 -0.6851677 -2.242257
+#>  5: KEGG_NUCLEOTIDE_EXCISION_REPAIR 0.001919386 0.01741098 -0.5785505 -2.157588
+#>  6:       KEGG_BASE_EXCISION_REPAIR 0.001934236 0.01741098 -0.5965607 -2.107505
+#>  7:      KEGG_PYRIMIDINE_METABOLISM 0.001841621 0.01741098 -0.4606911 -2.012965
+#>  8:            KEGG_MISMATCH_REPAIR 0.002008032 0.01741098 -0.6107380 -1.970065
+#>  9:             KEGG_RNA_POLYMERASE 0.001992032 0.01741098 -0.5731001 -1.955036
+#> 10:      KEGG_N_GLYCAN_BIOSYNTHESIS 0.003891051 0.02463808 -0.4815544 -1.828574
 #>     nMoreExtreme size                                    leadingEdge
 #>  1:            0   34             RFC5,RFC3,FEN1,MCM7,POLE2,DNA2,...
 #>  2:            0  121          ORC6,CDC7,CDC20,PKMYT1,CCNE1,ORC1,...
@@ -393,8 +396,8 @@ 
      
 #>  5:            0   41             RFC5,RFC3,POLE2,CCNH,RFC4,PCNA,...
 #>  6:            0   33           FEN1,HMGB1,MUTYH,UNG,POLE2,NEIL3,...
 #>  7:            0   90         POLR2D,DUT,POLE2,PRIM1,DTYMK,DHODH,...
-#>  8:            0   28 POLR2D,POLR3B,POLR2H,POLR2L,POLR3GL,POLR2J,...
-#>  9:            2   22              RFC5,RFC3,RFC4,PCNA,EXO1,RFC2,...
+#>  8:            0   22              RFC5,RFC3,RFC4,PCNA,EXO1,RFC2,...
+#>  9:            0   28 POLR2D,POLR3B,POLR2H,POLR2L,POLR3GL,POLR2J,...
 #> 10:            1   45         B4GALT2,DPM3,ALG14,FUT8,ALG6,MGAT2,...
      @@ -460,7 +463,7 @@

      -

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

      +

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

      diff --git a/docs/articles/TutorialOTTER_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/TutorialOTTER_files/figure-html/unnamed-chunk-15-1.png index 1a50f734..e41fc90a 100644 Binary files a/docs/articles/TutorialOTTER_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/TutorialOTTER_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 5083476f..a9cfd584 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ netZooR - 1.0.4 + 1.1.16
      @@ -130,6 +130,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

    + +
  • + Changelog
      • @@ -192,7 +195,7 @@

      All vignettes

      -

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

      +

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

      diff --git a/docs/articles/pandaR.html b/docs/articles/pandaR.html index c6a45631..b2d6b04f 100644 --- a/docs/articles/pandaR.html +++ b/docs/articles/pandaR.html @@ -31,7 +31,7 @@ netZooR - 1.0.4 + 1.1.16
      @@ -90,6 +90,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization
    + +
  • + Changelog
      • @@ -135,7 +138,7 @@

      Example

      An example dataset derived from a subset of stress-induced Yeast is available by running

      -library(netZooR)
      +library(netZooR) 
      ## Loading required package: igraph
      ## Warning: package 'igraph' was built under R version 4.1.2
      ## 
@@ -265,7 +268,7 @@ 
      
 
 
       
      
-  
      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.
      
+  
      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.
      
 
      
 
 
      
diff --git a/docs/articles/pandaRApplicationinGTExData.html b/docs/articles/pandaRApplicationinGTExData.html
index b208f7d6..908c5778 100644
--- a/docs/articles/pandaRApplicationinGTExData.html
+++ b/docs/articles/pandaRApplicationinGTExData.html
@@ -31,7 +31,7 @@
       
       
         netZooR
-        1.0.4
+        1.1.16
       
     
      
 
@@ -90,6 +90,9 @@
       YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization
    + +
  • + Changelog
      • @@ -147,7 +150,7 @@

      Load packages

      @@ -288,7 +291,7 @@

      Plot the top differential edges betwen LCL and WB

       # Select the top differential edge weights betweeen LCL and whole blood
-diffRes <- pandaDiffEdges(lcl_vis, wb_vis, condition_name="LCL")
+diffRes <- pandaDiffEdges(lcl_vis, wb_vis, condition_name="LCL")
 head(diffRes)
 # Number of differential edges is:
 nrow(diffRes)
@@ -343,19 +346,19 @@ 
      
 fgseaRes <- fgsea(pathways, degreeDiff_all, minSize=15, maxSize=500, nperm=1000)
 head(fgseaRes)
 #>                                          pathway        pval       padj
-#> 1:               KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.036407767 0.10558252
-#> 2:                  KEGG_CITRATE_CYCLE_TCA_CYCLE 0.001821494 0.01648352
-#> 3:                KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.110132159 0.22544701
-#> 4: KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.639198218 0.72693131
-#> 5:          KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.042889391 0.11660553
-#> 6:                     KEGG_GALACTOSE_METABOLISM 0.039130435 0.10950283
+#> 1:               KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.029850746 0.08991319
+#> 2:                  KEGG_CITRATE_CYCLE_TCA_CYCLE 0.001831502 0.01749271
+#> 3:                KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.083885210 0.17792202
+#> 4: KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.648230088 0.71807684
+#> 5:          KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.037444934 0.10402654
+#> 6:                     KEGG_GALACTOSE_METABOLISM 0.025641026 0.08391204
 #>            ES        NES nMoreExtreme size
-#> 1:  0.3355458  1.4089240           14   58
-#> 2: -0.5923935 -2.0223405            0   29
-#> 3:  0.4235984  1.3503798           49   21
-#> 4:  0.2675875  0.8668447          286   22
-#> 5:  0.4168076  1.4779398           18   30
-#> 6:  0.4491757  1.5179036           17   25
+#> 1:  0.3355458  1.4197869           11   58
+#> 2: -0.5923935 -2.0056899            0   29
+#> 3:  0.4235984  1.3970008           37   21
+#> 4:  0.2675875  0.8884628          292   22
+#> 5:  0.4168076  1.5152490           16   30
+#> 6:  0.4491757  1.5737014           11   25
 #>                                        leadingEdge
 #> 1:         ALDH3B1,LDHAL6A,PGM1,PKM,ALDOA,ENO1,...
 #> 2:              MDH2,CS,DLST,SDHD,IDH3B,SUCLG2,...
@@ -368,27 +371,27 @@ 
      
 # Get the top 10 significant pathways enriched for genes having lower targeting in LCLs  
 sig[order(sig$NES)[1:10],]
 #>                              pathway        pval       padj         ES
-#>  1:                 KEGG_SPLICEOSOME 0.001574803 0.01648352 -0.6155980
-#>  2:                    KEGG_RIBOSOME 0.001633987 0.01648352 -0.6438056
-#>  3:             KEGG_DNA_REPLICATION 0.001779359 0.01648352 -0.7301502
-#>  4:                  KEGG_CELL_CYCLE 0.001582278 0.01648352 -0.5352336
-#>  5:  KEGG_NUCLEOTIDE_EXCISION_REPAIR 0.001757469 0.01648352 -0.5896497
-#>  6:              KEGG_PROTEIN_EXPORT 0.001808318 0.01648352 -0.6735362
-#>  7: KEGG_AMINOACYL_TRNA_BIOSYNTHESIS 0.001718213 0.01648352 -0.5489421
-#>  8:     KEGG_CITRATE_CYCLE_TCA_CYCLE 0.001821494 0.01648352 -0.5923935
-#>  9: KEGG_BASAL_TRANSCRIPTION_FACTORS 0.001773050 0.01648352 -0.5641948
-#> 10:             KEGG_MISMATCH_REPAIR 0.007233273 0.03595970 -0.5977217
+#>  1:                 KEGG_SPLICEOSOME 0.001647446 0.01749271 -0.6155980
+#>  2:                    KEGG_RIBOSOME 0.001663894 0.01749271 -0.6438056
+#>  3:             KEGG_DNA_REPLICATION 0.001798561 0.01749271 -0.7301502
+#>  4:                  KEGG_CELL_CYCLE 0.001626016 0.01749271 -0.5352336
+#>  5:  KEGG_NUCLEOTIDE_EXCISION_REPAIR 0.001712329 0.01749271 -0.5896497
+#>  6:              KEGG_PROTEIN_EXPORT 0.001818182 0.01749271 -0.6735362
+#>  7: KEGG_AMINOACYL_TRNA_BIOSYNTHESIS 0.001733102 0.01749271 -0.5489421
+#>  8:     KEGG_CITRATE_CYCLE_TCA_CYCLE 0.001831502 0.01749271 -0.5923935
+#>  9: KEGG_BASAL_TRANSCRIPTION_FACTORS 0.001795332 0.01749271 -0.5641948
+#> 10:             KEGG_MISMATCH_REPAIR 0.001818182 0.01749271 -0.5977217
 #>           NES nMoreExtreme size                                   leadingEdge
-#>  1: -2.808508            0  116 SRSF6,SRSF3,SRSF7,HNRNPA1L2,PRPF38A,PPIL1,...
-#>  2: -2.724798            0   80      RPS2,RPL23A,RPL19,RPS12,RPS17,RPL10A,...
-#>  3: -2.613218            0   34           RFC3,RFC5,RPA2,POLE3,PRIM1,PCNA,...
-#>  4: -2.454800            0  121         YWHAQ,ORC6,DBF4,ANAPC10,BUB3,WEE1,...
-#>  5: -2.182026            0   41            XPA,RFC3,RFC5,RPA2,POLE3,ERCC8,...
-#>  6: -2.136133            0   22      SRP9,IMMP1L,HSPA5,SEC11C,OXA1L,SPCS2,...
-#>  7: -2.028489            0   40         MARS2,NARS,YARS,FARS2,YARS2,NARS2,...
-#>  8: -2.022340            0   29            MDH2,CS,DLST,SDHD,IDH3B,SUCLG2,...
-#>  9: -1.960503            0   31          TAF4,TAF7,TAF9,GTF2E1,GTF2F2,TBP,...
-#> 10: -1.895686            3   22             RFC3,RFC5,RPA2,PCNA,MSH2,RPA1,...
      +#> 1: -2.762220 0 116 SRSF6,SRSF3,SRSF7,HNRNPA1L2,PRPF38A,PPIL1,... +#> 2: -2.721909 0 80 RPS2,RPL23A,RPL19,RPS12,RPS17,RPL10A,... +#> 3: -2.594473 0 34 RFC3,RFC5,RPA2,POLE3,PRIM1,PCNA,... +#> 4: -2.422663 0 121 YWHAQ,ORC6,DBF4,ANAPC10,BUB3,WEE1,... +#> 5: -2.212853 0 41 XPA,RFC3,RFC5,RPA2,POLE3,ERCC8,... +#> 6: -2.146583 0 22 SRP9,IMMP1L,HSPA5,SEC11C,OXA1L,SPCS2,... +#> 7: -2.036029 0 40 MARS2,NARS,YARS,FARS2,YARS2,NARS2,... +#> 8: -2.005690 0 29 MDH2,CS,DLST,SDHD,IDH3B,SUCLG2,... +#> 9: -1.965811 0 31 TAF4,TAF7,TAF9,GTF2E1,GTF2F2,TBP,... +#> 10: -1.904960 0 22 RFC3,RFC5,RPA2,PCNA,MSH2,RPA1,...

      @@ -451,7 +454,7 @@

      -

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

      +

      Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

      diff --git a/docs/articles/pandaRApplicationinGTExData_files/figure-html/unnamed-chunk-14-1.png b/docs/articles/pandaRApplicationinGTExData_files/figure-html/unnamed-chunk-14-1.png index 7e51e1db..7feac827 100644 Binary files a/docs/articles/pandaRApplicationinGTExData_files/figure-html/unnamed-chunk-14-1.png and b/docs/articles/pandaRApplicationinGTExData_files/figure-html/unnamed-chunk-14-1.png differ diff --git a/docs/articles/yarn.html b/docs/articles/yarn.html index 3e1bdfb3..6aba91f8 100644 --- a/docs/articles/yarn.html +++ b/docs/articles/yarn.html @@ -31,7 +31,7 @@ netZooR - 1.0.4 + 1.1.16
      @@ -90,6 +90,9 @@ YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

    + +
  • + Changelog
      • @@ -115,7 +118,7 @@

      YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization

      Joseph N. Paulson & John Quackenbush

      -

      2022-06-27

      +

      2022-08-16

      Source: vignettes/yarn.Rmd @@ -176,13 +179,13 @@

    • First always remember to have the library loaded.
      • -library(netZooR)
      +library(netZooR)
      1. Download the GTEx gene count data as an ExpressionSet object or load the sample skin dataset.

      For computational reasons we load the sample skin data instead of having the user download the

      -library(netZooR)
+library(netZooR)
 load("skin.rdata")
      1. Check mis-annotation of gender or other phenotypes using group-specific genes
        2. @@ -270,9 +273,9 @@

        ## [8] base ## ## other attached packages: -## [1] RColorBrewer_1.1-2 netZooR_1.0.4 yarn_1.18.0 +## [1] RColorBrewer_1.1-2 netZooR_1.1.16 yarn_1.18.0 ## [4] pandaR_1.19.5 Biobase_2.52.0 BiocGenerics_0.38.0 -## [7] reticulate_1.22 igraph_1.3.2 +## [7] reticulate_1.22 igraph_1.3.4 ## ## loaded via a namespace (and not attached): ## [1] utf8_1.2.2 proto_1.0.0 @@ -383,7 +386,7 @@

        -

        Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Deborah Weighill.

        +

        Developed by Marouen Ben Guebila, Tian Wang, John Platig, Marieke Kuijjer, Megha Padi, Rebekka Burkholz, Des Weighill.

        diff --git a/docs/authors.html b/docs/authors.html index 66aacea7..db9b337b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -6,7 +6,7 @@ -Authors • netZooR +Citation and Authors • netZooR @@ -39,7 +39,7 @@ - + @@ -58,7 +58,7 @@ -
        +

    + +
  • + Changelog
      • @@ -151,17 +154,31 @@
      +
      +

      Citation

      + Source: inst/CITATION +
      + +

      Ben Guebila, M, Wang, T., Quackenbush, J. The Network Zoo: a multilingual package for the inference and analysis of biological networks bioRxiv, 2022

      + 
      @Article{,
+  title = {The Network Zoo: a multilingual package for the inference and analysis of biological networks},
+  author = {Marouen Ben Guebila and Tian Wang and John Quackenbush},
+  year = {2022},
+  journal = {bioRxiv},
+  doi = {10.1101/2022.05.30.494077},
+}
      +

      Authors

      • -

        Marouen Ben Guebila. Author, maintainer. +

        Marouen Ben Guebila. Author, maintainer.

      • -

        Tian Wang. Author. +

        Tian Wang. Author.

      • @@ -169,11 +186,11 @@

        Authors

      • -

        Marieke Kuijjer. Author. +

        Marieke Kuijjer. Author.

      • -

        Megha Padi. Author. +

        Megha Padi. Author.

      • @@ -181,7 +198,11 @@

        Authors

      • -

        Deborah Weighill. Author. +

        Des Weighill. Author. +

        +
        • +
      • +

        Kate Shutta. Contributor.

      @@ -194,7 +215,7 @@

      Authors