is.active: Interrogate "active" status of a given geneset.

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

Interrogate "active" status of a given geneset.

Description

Returns the active status of genesets, which are specified by their collection,name compound keys. This function is vectorized and supports query of multiple gene sets at a time. If a requested collection,name gene set doesn't exist, this throws an error.

Usage

is.active(x, i, j)

Arguments

x	GeneSetDb()
i	collection of geneset(s)
j	name of geneset(s) (must be same length as i.

Value

logical indicating if geneset is active. throws an error if any requested geneset does not exist in x.

Examples

dge.stats <- exampleDgeResult()
y <- exampleExpressionSet(do.voom = FALSE)
gdb <- conform(exampleGeneSetDb(), y, min.gs.size = 10)
# size 9 geneset:
geneSet(gdb, "c2", "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA")
is.active(gdb, "c2", "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA")
# geneset with >100 genes
is.active(gdb, "c7", "GSE3982_MAC_VS_NEUTROPHIL_LPS_STIM_DN")

lianos/sparrow documentation built on Dec. 8, 2024, 2:19 a.m.