readOpenMSFile {wrProteo}

Read csv files exported by OpenMS

Description

Protein quantification results form OpenMS which were exported as .csv can be imported and relevant information extracted. Peptide data get summarized by protein by top3 or sum methods. The final output is a list containing the elements: $annot, $raw, $quant ie normaized final quantifications, or returns data.frame with entire content of file if separateAnnot=FALSE.

Usage

readOpenMSFile(
  fileName = NULL,
  path = NULL,
  normalizeMeth = "median",
  refLi = NULL,
  sampleNames = NULL,
  quantCol = "Intensity",
  sumMeth = "top3",
  minPepNo = 1,
  protNaCol = "ProteinName",
  separateAnnot = TRUE,
  plotGraph = TRUE,
  tit = "OpenMS",
  wex = 1.6,
  specPref = c(conta = "LYSC_CHICK", mainSpecies = "OS=Homo sapiens"),
  silent = FALSE,
  debug = 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)

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

sampleNames

(character) new column-names for quantification data (by default the names from files with spectra will be used)

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

sumMeth

(character) method for summarizing peptide data (so far 'top3' and 'sum' available)

minPepNo

(integer) minumun number of peptides to be used for retruning quantification

protNaCol

(character) column name to be read/extracted for the annotation section (default "ProteinName")

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

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

debug

(logical) display additional messages for debugging

callFrom

(character) allow easier tracking of message(s) produced

Details

This function has been developed based on the OpenMS peptide-identification and label-free-quantification module. Csv input files may also be compresses as .gz.

Note: With this version the information about protein-modifications (PTMs) may not yet get exploited fully.

Value

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

See Also

read.table, normalizeThis) , readMaxQuantFile, readProlineFile, readProtDiscovFile

Examples

path1 <- system.file("extdata", package="wrProteo")
fiNa <- "OpenMS_tiny.csv.gz"
dataOM <- readOpenMSFile(file=fiNa, path=path1, tit="tiny OpenMS example")
summary(dataOM$quant)