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choijamts • 0@17bdf99c
Last seen 21 months ago
I wanted to get background gene lists of each pathway from string_db$get_enrichment() function.
But in the documentation https://bioconductor.org/packages/devel/bioc/manuals/STRINGdb/man/STRINGdb.pdf there were no information about it.
Here is my workflow: #1. Here I accessed to the string-db database and store it into object. library(STRINGdb) string_db <- STRINGdb$new( version="11", species=7227, score_threshold=400, input_directory="") #2. And here i tried to get all of the string id and gene names from stringdb #database and stored in "cc" object. cc <- string_db$get_aliases() head(cc) # STRING_id alias #1 7227.FBpp0070001 CG9570 #2 7227.FBpp0070002 Or19b dim(cc) # 750629 2 #3. As you can see there is huge number of gene lists, so lets get 50 of them for #get_enrichment analysis. cc_filter <- cc[1:50, 1:2] # First 50 genes GOenrichment <- string_db$get_enrichment(cc_filter, category = "Component") #dim(GOenrichment) #  1 10 # As you can see we got 1 pathway from get_enrichment() GO:CC function. # Lets check result #category term number_of_genes number_of_genes_in_background ncbiTaxonId inputGenes preferredNames p_value fdr description #1 Component GO.0090575 4 87 7227 ac,sc,l(1)sc,ase ac,sc,l(1)sc,ase 0.00031 0.028 RNA polymerase II transcription factor complex
As you see here, we got 1 pathway and 10 variables, one of these variable is "number_of_genes_in_background". But the problem is that i couldn't get the background "gene list" for this pathway. Is there anyway to see that one?