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.
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
)(character) name of file to be read (default 'proteinGroups.txt' as typically generated by MaxQuant in txt folder)
(character) path of file to be read
(character) normalization method (will be sent to normalizeThis)
(character) new column-names for quantification data (ProteomeDiscoverer does not automatically use file-names from spectra)
(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
(logical) if TRUE output will be organized as list with $annot, $abund for initial/raw abundance values and $quant with final normalized quantitations
(character) custom title to plot
(character) depreciated custom title to plot, please use 'tit'
(integer) relative expansion factor of the violin-plot (will be passed to vioplotW)
(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)
(logical) optional plot of type vioplot of initial and normalized data (using normalizeMeth); if integer, it will be passed to layout when plotting
(logical) suppress messages
(character) allow easier tracking of message(s) produced
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
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.
# NOT RUN {
path1 <- system.file("extdata", package="wrProteo")
fiNa <- "tinyMC.RData"
dataMC <- readMassChroQFile(file=fiNa, path=path1)
# }
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