diff --git a/README.html b/README.html index aeb364b..a896d6c 100644 --- a/README.html +++ b/README.html @@ -717,7 +717,55 @@

eheat

-

Other non-lazied operations: | Operations | BPCells | BPCellsArray | Note | | —————– | —————- | ———————— | —————- | | row/col summarize | matrix_stats | matrix_stats | | | row summarize | rowSums,rowMeans | rowSums,rowMeans,rowVars | | | col summarize | colSums,colMeans | colSums,colMeans,colVars | | | Multiplication | %% | %% | For some methods | | Crossproduct | | crossprod | For some methods | | svd | svds | SpectraParam | |

+

Other non-lazied operations:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OperationsBPCellsBPCellsArrayNote
row/col summarizematrix_statsmatrix_stats
row summarizerowSums,rowMeansrowSums,rowMeans,rowVars
col summarizecolSums,colMeanscolSums,colMeans,colVars
Multiplication%*%%*%For some methods
CrossproductcrossprodFor some methods
svdsvdsSpectraParam

Matrix Storage Format

BPCells provide three format: 1. Directory of files 2. Hdf5 file 3. R object Details see: https://bnprks.github.io/BPCells/articles/web-only/bitpacking-format.html

BPCellsArray only implement the Directory of files format, which is used across the package of BPCells.

@@ -821,7 +869,7 @@

Matrix Storage Format

#> Storage order: column major #> #> Queued Operations: -#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e +#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae

If you do delayed operations with this assay, the class may be changed, that’s because all of BPCells operations are lazy, no real work is performed on the matrix until the result needs to be returned as an R object or written to disk. You can coerce it into a dense matrix or dgCMatrix to get a actual R object.

assay(sce, "counts")[1:10, 1:10]
 #> 10 x 10 DelayedMatrix object with class BPCellsSubsetMatrix
@@ -833,7 +881,7 @@ 
Matrix Storage Format

 #> Storage order: column major
 #> 
 #> Queued Operations:
-#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e
+#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae
 #> 2. Select rows: 1, 2 ... 10 and cols: 1, 2 ... 10
 as.matrix(assay(sce, "counts")[1:10, 1:10])
 #>           Cell_001 Cell_002 Cell_003 Cell_004 Cell_005 Cell_006 Cell_007
@@ -887,7 +935,7 @@ 
Matrix Storage Format

 #> Storage order: column major
 #> 
 #> Queued Operations:
-#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e
+#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae
 #> 2. Scale columns by 0.984, 1.05 ... 1
 #> 3. Transform log1p
 #> 4. Scale by 1.44
diff --git a/README.md b/README.md index 20e5ba1..256ded3 100644 --- a/README.md +++ b/README.md @@ -40,13 +40,16 @@ Here is a summarized delayed operations in BPCells: | log(1+x) | `log1p`,`log1p_slow` | `log1p`,`log1p_slow` | | Power | `pow_slow`,`^` | `pow_slow`,`^` | -Other non-lazied operations: | Operations | BPCells | BPCellsArray | -Note | | —————– | —————- | ———————— | —————- | | row/col summarize | -matrix\_stats | matrix\_stats | | | row summarize | rowSums,rowMeans | -rowSums,rowMeans,rowVars | | | col summarize | colSums,colMeans | -colSums,colMeans,colVars | | | Multiplication | %*% | %*% | For some -methods | | Crossproduct | | crossprod | For some methods | | svd | svds -| SpectraParam | | +Other non-lazied operations: + +| Operations | BPCells | BPCellsArray | Note | +| ----------------- | ---------------- | ------------------------ | ---------------- | +| row/col summarize | matrix\_stats | matrix\_stats | | +| row summarize | rowSums,rowMeans | rowSums,rowMeans,rowVars | | +| col summarize | colSums,colMeans | colSums,colMeans,colVars | | +| Multiplication | %\*% | %\*% | For some methods | +| Crossproduct | | crossprod | For some methods | +| svd | svds | SpectraParam | | ## Matrix Storage Format @@ -175,7 +178,7 @@ assay(sce, "counts") #> Storage order: column major #> #> Queued Operations: -#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e +#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae ``` If you do delayed operations with this assay, the class may be changed, @@ -195,7 +198,7 @@ assay(sce, "counts")[1:10, 1:10] #> Storage order: column major #> #> Queued Operations: -#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e +#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae #> 2. Select rows: 1, 2 ... 10 and cols: 1, 2 ... 10 as.matrix(assay(sce, "counts")[1:10, 1:10]) #> Cell_001 Cell_002 Cell_003 Cell_004 Cell_005 Cell_006 Cell_007 @@ -260,7 +263,7 @@ assay(sce, "logcounts") #> Storage order: column major #> #> Queued Operations: -#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e +#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae #> 2. Scale columns by 0.984, 1.05 ... 1 #> 3. Transform log1p #> 4. Scale by 1.44 diff --git a/vignettes/BPCellsArray.Rmd b/vignettes/BPCellsArray.Rmd index 5737ee4..4675808 100644 --- a/vignettes/BPCellsArray.Rmd +++ b/vignettes/BPCellsArray.Rmd @@ -48,6 +48,7 @@ Here is a summarized delayed operations in BPCells: Other non-lazied operations: + | Operations | BPCells | BPCellsArray | Note | | ----------------- | ---------------- | ------------------------ | ---------------- | | row/col summarize | matrix_stats | matrix_stats | |