runWebGestaltGSEA: workflow for GSEA

In protViz/fgczgseaora: ORA, sigORA and GSEA functionalities for proteomic data

Description

workflow for GSEA

Usage

runWebGestaltGSEA(
  data,
  fpath,
  ID_col = "UniprotID",
  score_col = "estimate",
  organism = "hsapiens",
  target = "geneontology_Biological_Process",
  nperm = 10,
  outdir = "GSEA",
  interestGeneType = "uniprotswissprot",
  contrast_name = fpath
)

Arguments

data	data
fpath	file path to write to
ID_col	column name containing IDs
score_col	column name containing estimates
organism	organism
target	target database, default: geneontology_Biological_Process
nperm	number of permutations
outdir	output directory
interestGeneType	what type of identifier default : "uniprotswissprot"
contrast_name	for pretty printing

protViz/fgczgseaora documentation built on Dec. 14, 2021, 9:22 p.m.