GeneSet_Exprs: Exports Expression data for a GeneSet of interest

In Rvirgenslane/Hotgenes: For Visualizing Differential Expression Analysis

Description

Exports Expression data for a GeneSet of interest

Usage

GeneSet_Exprs(
  GSEA_Hotgenes = NULL,
  normalizedData = 1,
  contrastID = 1,
  pathwayID = 1
)

Arguments

GSEA_Hotgenes	HotgenesObj appended by BatchGSEA function
normalizedData	indicates the normalized data in HotgenesObj to return.
contrastID	contrast selection
pathwayID	String or numeric index indicating the desired pathway

Value

Expresion data

Examples

Example_Hotgenes_dir<-system.file("extdata",
"Example_Hotgenes.Rdata",
package = "Hotgenes", mustWork = TRUE)
load(Example_Hotgenes_dir)
library(msigdbr)
m_df = msigdbr(species = "Homo sapiens", category = "C5", subcategory = "BP")
qbat<-BatchGSEA(m_df= m_df, HotgenesObj=Example_Hotgenes)
expsD<-GeneSet_Exprs(GSEA_Hotgenes=qbat)
library(pheatmap)
pheatmap(expsD$E,scale = "row",
main=expsD$Main)

Rvirgenslane/Hotgenes documentation built on Aug. 22, 2020, 2:11 a.m.