rnagage: rnagage function

Description Usage Arguments Value Examples

View source: R/rnagage.R

Description

Uses gage to find enriched pathways from the RNAseq differential gene analysis

Usage

1
rnagage(deg, lookup)

Arguments

lookup

data frame of entrez ID and gene name pairs

rnadeg

data frame generated by topTable of limma output

Value

data frame of RNAseq values for only patients in the high and low gene expression groups

Examples

1
2
3
4
5
data(skcm)
gene <- "SOX10"
sox10.pat <- rnasubset(pat, rna, gene, 10)
sox10.deg <- rnadeg(sox10.pat, rna)
sox10.gage <- rnagage(sox10.deg, lookup)

pcheng84/TCGAbrowser documentation built on Sept. 7, 2021, 8:28 p.m.