Mice RNA-seq pathway analysis

[samanehgholami]

Can I use this package for pathway enrichment analysis of Mice RNA-seq data?
I am new to RNA-seq analysis in Mice! I am searching for a package works in R (with KEGG mice or others), rather than online pathways enrichments and multiple copy, paste and finally analysis in Prism!
I will appreciate if you help me!
Thank you

[egeulgen]

Hello,

Yes, you can use pathfindR for mice data or any other organism. See this vignette

Particulary see here. You can use the following to analyze the data:

myeloma_output <- run_pathfindR(input = input_df,
                                convert2alias = FALSE,
                                gene_sets = "mmu_KEGG",
                                pin_name_path = "mmu_STRING")

[samanehgholami]

Hello,
Thank you very much. This helps me.
I will try this and will ask you if I need more help.

Thank you again.

[samanehgholami]

Hello,

I try to the package for mice, but i got these two errors even when i just want to run a sample:

gsets_list <- get_gene_sets_list(source = "KEGG",

•                              org_code = "mmu")
  

Error in loadNamespace(x) : there is no package called ‘KEGGREST’

myeloma_output <- run_pathfindR(input = myeloma_input,

•                             convert2alias = FALSE,
  

•                             gene_sets = "Custom",
  

•                             custom_genes = mmu_kegg_genes,
  

•                             custom_descriptions = mmu_kegg_descriptions,
  

•                             pin_name_path = path2SIF)
  

Error in pin_name_path %in% valid_opts[-length(valid_opts)] :
object 'path2SIF' not found

Please could you help me with this? I am sorry for asking many questions.

Thank you very much

[egeulgen]

You do not have to obtain the data manually, you can run the built-in data via:

output_df <- run_pathfindR(input = input_df,
                                convert2alias = FALSE,
                                gene_sets = "mmu_KEGG",
                                pin_name_path = "mmu_STRING")

[samanehgholami]

Ok thank you. Now it is working.

[samanehgholami]

Hello,

I try to use the list of gene I have and analyze them with pathfindR. I am really thankful for all your help.
I could run the samples you mentioned in package and all other articles you wrote and they work perfect.
But I can not analyze my data, a data frame of gene and adjusted P values.

sapply(upreg, class)
Gene.symbol logFC adj.P.Val
"character" "numeric" "numeric"
upreg_output <- run_pathfindR(upreg)

Testing input

Error in pathfindR::input_testing(input, p_val_threshold) :
p values must all be numeric

I got this error all the time that p values should be numeric! but they are. I changed them to numeric and as you see it is numeric. But I dont know why I get this.

I do appreciate if you help me again too. thank you

[egeulgen]

Can you try upreg<-as.data.frame(upreg ), tibbles sometimes cause an issue

[samanehgholami]

Dear EgeUlgen,
I also can send the data I have, if it can help. As i mentioned it is on mice but also we may need to check these genes in human pathways too.

Many thanks in advance.
Sama