runWebGestaltORA: workflow for ORA

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

Description

workflow for ORA

Usage

runWebGestaltORA(
  data,
  fpath,
  organism = "hsapiens",
  ID_col = "UniprotID",
  target = "geneontology_Biological_Process",
  threshold = 0.59,
  greater = TRUE,
  nperm = 10,
  score_col = "estimate",
  outdir = "WebGestalt_ORA",
  subdir_name = NULL,
  interestGeneType = "uniprotswissprot",
  contrast_name = fpath
)

Arguments

data	data
fpath	file path to write to
organism	organism
ID_col	column name containing IDs
target	target database, default: "geneontology_Biological_Process"
threshold	threshold for estimate
greater	indicating direction of threshold
nperm	number of permutations
score_col	column name containing estimates
outdir	output directory
subdir_name	subdirectory name
interestGeneType	what type of identifier default : "uniprotswissprot"
contrast_name	default fpath

protViz/prora documentation built on Dec. 12, 2021, 12:32 a.m.