| readProtDiscovFile {wrProteo} | R Documentation |
Read Tabulated Files Exported By ProteomeDiscoverer At Protein Level, Deprecated
Description
Depreciated old version of Protein identification and quantification results from
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.
Please use readProteomeDiscovererFile() from the same package instead !
Usage
readProtDiscovFile(
fileName,
path = NULL,
normalizeMeth = "median",
sampleNames = NULL,
read0asNA = TRUE,
quantCol = "^Abundances*",
annotCol = NULL,
contamCol = "Contaminant",
refLi = NULL,
separateAnnot = TRUE,
FDRCol = list(c("^Protein.FDR.Confidence", "High"), c("^Found.in.Sample.", "High")),
gr = NULL,
sdrf = NULL,
suplAnnotFile = TRUE,
groupPref = list(lowNumberOfGroups = TRUE),
specPref = c(conta = "CON_|LYSC_CHICK", mainSpecies = "OS=Homo sapiens"),
plotGraph = TRUE,
wex = 1.6,
titGraph = "Proteome Discoverer",
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, defaults to |
sampleNames |
(character) custom column-names for quantification data (ProteomeDiscoverer does not automatically use file-names from spectra); this argument has priority over |
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 |
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.
If a column named |
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 |
FDRCol |
(list) optional indication to search for protein FDR information |
gr |
(character or factor) custom defined pattern of replicate association, will override final grouping of replicates from |
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 element may give futher indicatations for automatic organization of groups of replicates.
Besides, the output from |
suplAnnotFile |
(logical or character) optional reading of supplemental files produced by ProteomeDiscoverer; however, if |
groupPref |
(list) additional parameters for interpreting meta-data to identify structure of groups (replicates), will be passed to |
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 |
plotGraph |
(logical or integer) optional plot of type vioplot of initial and normalized data (using |
wex |
(integer) relative expansion factor of the violin-plot (will be passed to |
titGraph |
(character) custom title to plot of distribution of quantitation values |
silent |
(logical) suppress messages |
debug |
(logical) additional messages for debugging |
callFrom |
(character) allow easier tracking of messages produced |
Details
This function has been replaced by readProteomeDiscovererFile (from the same package) !
The syntax and strcuture of output has remained the same, you can simply replace the name of the function called.
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.
Using the argument suplAnnotFile it is possible to specify a specific file (or search for default file) to read for extracting file-names as sample-names and other experiment realted information.
If a column named contamCol is found, the data will be lateron filtered to remove all contaminants, set to NULL for keeping all contaminants
This function replaces the depreciated function readPDExport.
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
and $notes; or if separateAnnot=FALSE the function returns a data.frame with annotation and quantitation only
See Also
read.table, normalizeThis) , readMaxQuantFile, readProlineFile, readFragpipeFile
Examples
path1 <- system.file("extdata", package="wrProteo")
fiNa <- "tinyPD_allProteins.txt.gz"
## Please use the function readProteinDiscovererFile(), as shown below (same syntax)
dataPD <- readProteomeDiscovererFile(file=fiNa, path=path1, suplAnnotFile=FALSE)
summary(dataPD$quant)