gseaI: Function "gseaI"

In Coraline66/RNASeqAnalysis: Perform RNASeq Data Analysis

Description

This function performs GSEA analysis.

Usage

gseaI(res_anno, geneEX, geneSet, condition, N, n1, n2, Min, Max)

Arguments

res_anno	a data frame with the result of DESeq along with gene annotation
geneEX	normalized gene expression matrix based on ensembl IDs
geneSet	a gene set list, consisting of entrezgene IDs
condition	a string character representing the group condition
N	a numeric variable indicating the number of total samples
n1	a numeric variable indicating the number of samples for one of the group condition
n2	a numeric variable indicating the number of samples for the other group condition
Min	a numeric variable representing the minimum size of pathway accepted for GSEA
Max	a numeric variable representing the maximum size of pathway accepted for GSEA

Value

a list of gene rank based on entrezgene ID, result of GSEA and an ExpressionSet object of normalized counts matrix based on entrezgene IDs.

Coraline66/RNASeqAnalysis documentation built on Nov. 25, 2019, 8:03 a.m.