exportAsWombatP: Export As Wombat-P Set Of Files

In wrProteo: Proteomics Data Analysis Functions

Export As Wombat-P Set Of Files

Description

This function allows exporting objects created from wrProteo to the format of Wombat-P Wombat-P.

Usage

exportAsWombatP(
  wrProtObj,
  path = ".",
  combineFractions = "mean",
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

wrProtObj	(list produced by any import-function from wrProteo) object which will be exported as Wombat-P format
path	(character) the location where the data should be exorted to
combineFractions	(NULL or character (length=1)) if not NULL this assigns the method how multiple farctions should be combined (at this point only the method 'mean' is implemented)
silent	(logical) suppress messages
debug	(logical) display additional messages for debugging
callFrom	(character) allows easier tracking of messages produced

Value

This function creates a set of files (README.md, test_params.yml), plus a sud-directory containig file(s) (stand_prot_quant_method.csv); finally the function returns (NULL),

See Also

readMaxQuantFile, readProteomeDiscovererFile; moderTestXgrp or moderTest2grp

Examples

path1 <- system.file("extdata", package="wrProteo")
fiNa <- "proteinGroupsMaxQuant1.txt.gz"
specPr <- c(conta="conta|CON_|LYSC_CHICK", mainSpecies="YEAST", spike="HUMAN_UPS")
dataMQ <- readMaxQuantFile(path1, file=fiNa, specPref=specPr, tit="tiny MaxQuant")

exportAsWombatP(dataMQ, path=tempdir())

wrProteo documentation built on April 12, 2025, 1:16 a.m.