wrProteo: readProtDiscovFile – R documentation

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readProtDiscovFile

Read tabulated files exported by ProteomeDiscoverer

Description

Protein quantification results form Thermo ProteomeDiscoverer which were exported as tabulated text can be imported and relevant information extracted. The final output is a list containing 3 elements: $annot, $raw and optional $quant, or returns data.frame with entire content of file if separateAnnot=FALSE.

Usage

readProtDiscovFile(
  fileName,
  path = NULL,
  normalizeMeth = "median",
  sampleNames = NULL,
  read0asNA = TRUE,
  quantCol = "^Abundances*",
  annotCol = NULL,
  contamCol = "Contaminant",
  refLi = NULL,
  separateAnnot = TRUE,
  plotGraph = TRUE,
  tit = "Proteome Discoverer",
  graphTit = NULL,
  wex = 1.6,
  specPref = c(conta = "CON_|LYSC_CHICK", mainSpecies = "OS=Homo sapiens"),
  silent = FALSE,
  callFrom = NULL
)

Arguments

`fileName`	(character) name of file to be read
`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)
`read0asNA`	(logical) decide if initial quntifications at 0 should be transformed to NA
`quantCol`	(character or integer) exact col-names, or if length=1 content of `quantCol` will be used as pattern to search among column-names for $quant using `grep`
`annotCol`	(character) column names to be read/extracted for the annotation section (default c("Accession","Description","Gene","Contaminant","Sum.PEP.Score","Coverage....","X..Peptides","X..PSMs","X..Unique.Peptides", "X..AAs","MW..kDa.") )
`contamCol`	(character or integer, length=1) which columns should be used for contaminants marked by ProteomeDiscoverer
`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
`plotGraph`	(logical) optional plot of type vioplot of initial and normalized data (using `normalizeMeth`); if integer, it will be passed to `layout` when plotting
`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`)
`silent`	(logical) suppress messages
`callFrom`	(character) allow easier tracking of message(s) produced

Details

This function has been developed using Thermo ProteomeDiscoverer versions 2.2 to 2.5. The format of resulting files at export also depends which columns are chosen as visible inside ProteomeDiscoverer and subsequently get chosen for export. Please make sure that 'RawAbundance' is chosen, too. This function replaces the depreciated function readPDExport.

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 <- "tinyPD_allProteins.txt.gz"
dataPD <- readProtDiscovFile(file=fiNa, path=path1)
summary(dataPD$quant)

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release