readMzTabData {MSnbase} | R Documentation |
This function can be used to create an
"MSnSet"
by reading and parsing an
mzTab
file. The metadata section is always used to populate
the MSnSet
's experimentData()@other$mzTab
slot.
readMzTabData(file, what = c("PRT", "PEP", "PSM"), version = c("1.0", "0.9"), verbose = isMSnbaseVerbose())
file |
A |
what |
One of |
version |
A |
verbose |
Produce verbose output. |
An instance of class MSnSet
.
Laurent Gatto
See MzTab
and MSnSetList
for
details about the inners of readMzTabData
.
testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/1_0-Proteomics-Release/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt" prot <- readMzTabData(testfile, "PRT") prot head(fData(prot)) head(exprs(prot)) psms <- readMzTabData(testfile, "PSM") psms head(fData(psms))