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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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Pathfinder attaches KEGG organism ID to gene IDs #209

Closed Rohit-Satyam closed 1 month ago

Rohit-Satyam commented 1 month ago

Describe the bug Unlike version 2.3.1, the latest version appends the "pfa" IDs and I was wondering if this is intentional or accidental?

> gsets_list2.3$gene_sets$pfa00010
 [1] "PF3D7_0624000" "PF3D7_1436000" "PF3D7_0915400" "PF3D7_1444800" "PF3D7_1439900"
 [6] "PF3D7_0318800" "PF3D7_1462800" "PF3D7_0922500" "PF3D7_1120100" "PF3D7_1015900"
[11] "PF3D7_1037100" "PF3D7_0626800" "PF3D7_1124500" "PF3D7_1446400" "PF3D7_1020800"
[16] "PF3D7_1232200" "PF3D7_0815900" "PF3D7_0627800" "PF3D7_1012500" "PF3D7_1342800"
> gsets_list$gene_sets$pfa00010
 [1] "pfa:PF3D7_1444800" "pfa:PF3D7_1124500" "pfa:PF3D7_1446400" "pfa:PF3D7_1020800"
 [5] "pfa:PF3D7_0626800" "pfa:PF3D7_1037100" "pfa:PF3D7_1015900" "pfa:PF3D7_1120100"
 [9] "pfa:PF3D7_1462800" "pfa:PF3D7_0318800" "pfa:PF3D7_1439900" "pfa:PF3D7_0915400"
[13] "pfa:PF3D7_1436000" "pfa:PF3D7_1012500" "pfa:PF3D7_0624000" "pfa:PF3D7_0815900"
[17] "pfa:PF3D7_1232200" "pfa:PF3D7_0922500" "pfa:PF3D7_1342800" "pfa:PF3D7_0627800"

To Reproduce

gsets_list <- get_gene_sets_list(source = "KEGG",
                                 org_code = "pfa")

Desktop (please complete the following information):

egeulgen commented 1 month ago

It is intentional. In the latest version, we updated this function so that get_kegg_gsets() now returns KEGG IDs so that the user can convert the returned identifiers using a more appropriate tool (e.g. BioMart) should they wish. The ID conversion is beyond the scope of this package.