wrProteo: readMassChroQFile – R documentation

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readMassChroQFile

Read tabulated files imported from MassChroQ

Description

Quantification results using MassChroQ should be initially treated using the R-package MassChroqR (both distributed by the PAPPSO at http://pappso.inrae.fr/) for initial normalization on peptide-level and combination of peptide values into protein abundances.

Usage

readMassChroQFile(
  fileName,
  path = NULL,
  normalizeMeth = "median",
  sampleNames = NULL,
  refLi = NULL,
  separateAnnot = TRUE,
  tit = "MassChroQ",
  graphTit = NULL,
  wex = NULL,
  specPref = c(conta = "CON_|LYSC_CHICK", mainSpecies = "OS=Homo sapiens"),
  plotGraph = TRUE,
  silent = FALSE,
  callFrom = NULL
)

Arguments

`fileName`	(character) name of file to be read (default 'proteinGroups.txt' as typically generated by MaxQuant in txt folder)
`path`	(character) path of file to be read
`normalizeMeth`	(character) normalization method (will be sent to `normalizeThis`)
`sampleNames`	(character) new column-names for quantification data (ProteomeDiscoverer does not automatically use file-names from spectra)
`refLi`	(character or integer) custom specify which line of data is main species, if character (eg 'mainSpe'), the column 'SpecType' in $annot will be searched for exact match of the (single) term given
`separateAnnot`	(logical) if `TRUE` output will be organized as list with `$annot`, `$abund` for initial/raw abundance values and `$quant` with final normalized quantitations
`tit`	(character) custom title to plot
`graphTit`	(character) depreciated custom title to plot, please use 'tit'
`wex`	(integer) relative expansion factor of the violin-plot (will be passed to `vioplotW`)
`specPref`	(character or list) define characteristic text for recognizing (main) groups of species (1st for comtaminants - will be marked as 'conta', 2nd for main species- marked as 'mainSpe', and optional following ones for supplemental tags/species - maked as 'species2','species3',...); if list and list-element has multiple values they will be used for exact matching of accessions (ie 2nd of argument `annotCol`)
`plotGraph`	(logical) optional plot of type vioplot of initial and normalized data (using `normalizeMeth`); if integer, it will be passed to `layout` when plotting
`silent`	(logical) suppress messages
`callFrom`	(character) allow easier tracking of message(s) produced

Details

The final output of this fucntion is a list containing 3 elements: $annot, $raw, $quant and $notes, or returns data.frame with entire content of file if separateAnnot=FALSE. Other list-elements remain empty to keep format compatible to other import functions.

This function has been developed using MassChroQ version 2.2 and R-package MassChroqR version 0.4.0. Both are distributed by the PAPPSO (http://pappso.inrae.fr/). When saving quantifications as RData, the ABUNDANCE_TABLE produced by mcq.get.compar(XICAB) should be used.

After import data get (re-)normalized according to normalizeMeth and refLi, and boxplots or vioplots drawn.

Value

list with $raw (initial/raw abundance values), $quant with final normalized quantitations, $annot, $counts an array with number of peptides, $quantNotes and $notes; or if separateAnnot=FALSE the function returns a data.frame with annotation and quantitation only

Examples

path1 <- system.file("extdata", package="wrProteo")
fiNa <- "tinyMC.RData"
dataMC <- readMassChroQFile(file=fiNa, path=path1)

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release