do_gsea_pod: Perform the Geneset Enrichment Analysis

In AliSajid/BioPathNet: BioPathNet: Three Pod Analysis System

Perform the Geneset Enrichment Analysis

Description

This function takes a BPNList object and performs a Geneset Enrichment Analysis and returns a BPNList object with the results of the GSEA

Usage

do_gsea_pod(
  bpn,
  species = "hsapiens",
  gmtfile = NULL,
  lower = NULL,
  upper = NULL,
  alpha = 0.05,
  minSize = 15,
  maxSize = 500,
  rankWithSignificance = FALSE,
  useFDR = TRUE
)

Arguments

bpn	BPNList An object of class BPNList created from prepare_data
species	character One of the species for which we provide current GMT pathways. Currently the valid species are hsapiens, mmusculus and rnorvegicus. Cannot be specified along with gmtfile
gmtfile	character A full path to a GMT File you would like to use. Cannot be specified along with species
lower	numeric The cutoff for down-regulated genes. If not specified, it takes the bottom 10% of the dataset
upper	numeric The cutoff for up-regulated genes. If not specified, it takes the top 10% of the dataset
alpha	numeric The Alpha value for statistical significance. Defaults to 0.05.
minSize	numeric The minimum number of genes that should be in a pathway for it to be included in the analysis
maxSize	numeric The maximum number of genes that should be in a pathway for it to be included in the analysis
rankWithSignificance	logical Whether to rank genes using p-values
useFDR	logical Whether to filter by adjusted p-value

Details

This function takes a BPNList object and performs a Geneset Enrichment Analysis and returns a BPNList object with the results of the GSEA

Value

An object of class BPNList with its gsea slot populated with the results

Examples

TRUE

AliSajid/BioPathNet documentation built on July 4, 2023, 6:40 a.m.