runSIGORA: workflow for sigORA

In protViz/fgcz.gsea.ora: ORA, sigORA and GSEA functionalities for proteomic data

Description

workflow for sigORA

Usage

runSIGORA(
  data,
  target = "GO",
  score_col = "estimate",
  ID_col = "UniprotID",
  threshold = 0.5,
  outdir = "sigORA",
  greater = TRUE,
  myGPSrepo = NULL,
  DEBUG = FALSE
)

Arguments

data	data
target	target database, default: "GO"
score_col	column name containing estimates
ID_col	column name containing IDs
threshold	threshold for estimate
outdir	output directory
greater	flag whether to filter > threshold or < threshold
myGPSrepo	gps repository
DEBUG	default FALSE, if TRUE, skip markdown generation

Examples

library(prora)
fc_estimates <- prora::exampleContrastData
filtered_dd <- get_UniprotID_from_fasta_header(fc_estimates, idcolumn = "protein_Id")
myGPSrepo <- makeGPS_wrappR(filtered_dd$UniprotID, target = "GO")

#usethis::use_data(myGPSrepo,overwrite = TRUE)
undebug(runSIGORA)
undebug(sigoraWrappR)
res <- runSIGORA(filtered_dd, myGPSrepo = prora::myGPSrepo, DEBUG=TRUE)

## Not run: 
rmarkdown::render(res$rmarkdownPath,
bookdown::html_document2(number_sections = FALSE),
params = res$sigoraData,
clean = TRUE)

## End(Not run)

protViz/fgcz.gsea.ora documentation built on Dec. 24, 2021, 9:47 a.m.