annotateGeneSetMembership {sparrow} | R Documentation |
This is helpful when you don't have a monsterly sized GeneSetDb. There will
be as many new columns added to x
as there are active genesets in gdb
.
annotateGeneSetMembership(x, gdb, x.ids = NULL, ...)
x |
A data.frame with genes/features in rows |
gdb |
A |
x.ids |
The name of the column in |
... |
parameters passed down into |
Returns the original x
with additional columns: each is a
logical vector that indicates membership for genesets defined in
gdb
.
vm <- exampleExpressionSet() gdb <- exampleGeneSetDb() mg <- seas(vm, gdb, design = vm$design, contrast = 'tumor') lfc <- logFC(mg) annotated <- annotateGeneSetMembership(lfc, gdb, 'feature_id') ## Show only genes that are part of 'HALLMARK_ANGIOGENESIS' geneset angio <- subset(annotated, `c2;;BIOCARTA_AGPCR_PATHWAY`)