genes-GSVA-method: gene method

In guokai8/scGSVA: GSVA and UCell signature enrichment analysis for single cell RNA seq

gene method

Description

gene method

Usage

## S4 method for signature 'GSVA'
genes(
  object,
  features,
  useTerm = TRUE,
  with.expr = TRUE,
  assay = NULL,
  slot = "counts"
)

Arguments

object	GSVA object
features	A vector of features to extract
useTerm	use Term or use id (default: TRUE)
with.expr	extract the expression value or not (default: TRUE)
assay	Assay to use in GSVA analysis ('RNA','SCT' or 'Spatial' if spatial transcriptomics)
slot	Specific assay data to get or set

Value

data.frame

Author(s)

Kai Guo

Examples

## Not run: 
data(pbmc_small)
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
res<-scgsva(pbmc_small, hsako)
head(genes(res,"Acute myeloid leukemia"))

## End(Not run)

guokai8/scGSVA documentation built on Nov. 15, 2024, 12:54 a.m.