readMassChroQFile {wrProteo}

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,
  titGraph = "MassChroQ",
  wex = NULL,
  specPref = c(conta = "CON_|LYSC_CHICK", mainSpecies = "OS=Homo sapiens"),
  gr = NULL,
  sdrf = NULL,
  suplAnnotFile = FALSE,
  groupPref = list(lowNumberOfGroups = TRUE),
  plotGraph = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

fileName

(character) name of file to be read (may be tsv, csv, rda or rdata); both US and European csv formats are supported

path

(character) path of file to be read

normalizeMeth

(character) normalization method (will be sent to normalizeThis)

sampleNames

(character) custom column-names for quantification data; this argument has priority over suplAnnotFile

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

titGraph

(character) custom title to plot of distribution of quantitation values

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)

gr

(character or factor) custom defined pattern of replicate association, will override final grouping of replicates from sdrf and/or suplAnnotFile (if provided)

sdrf

(character, list or data.frame) optional extraction and adding of experimenal meta-data: if character, this may be the ID at ProteomeExchange, the second & third elements may give futher indicatations for automatic organization of groups of replicates. Besides, the output from readSdrf or a list from defineSamples may be provided; if gr is provided, gr gets priority for grouping of replicates; if sdrfOrder=TRUE the output will be put in order of sdrf

suplAnnotFile

(logical or character) optional reading of supplemental files produced by ProteomeDiscoverer; however, if gr is provided, gr gets priority for grouping of replicates; if TRUE defaults to file '*InputFiles.txt' (needed to match information of sdrf) which can be exported next to main quantitation results; if character the respective file-name (relative or absolute path)

groupPref

(list) additional parameters for interpreting meta-data to identify structure of groups (replicates), will be passed to readSampleMetaData. May contain lowNumberOfGroups=FALSE for automatically choosing a rather elevated number of groups if possible (defaults to low number of groups, ie higher number of samples per group)

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

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages 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 generated in R as RData (with extension .rdata or .rda) using the R-packages associated with MassChroq, 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

This function returns 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

See Also

read.table, normalizeThis) , readProlineFile

Examples

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