PSMfilter {pepXMLTab} | R Documentation |
The PSMfilter() function filter the peptide identification based on user chosen paramter.
PSMfilter(PSMtab, pepFDR = 0.01, scorecolumn = "mvh", hitrank = 1, minpeplen = 6, decoyprefix = "rev_", ...)
PSMtab |
a data frame contain peptide identification from a pepXML file |
pepFDR |
filter the peptides based on this chosen FDR, default is 0.01. |
scorecolumn |
which column is chosen to calculate FDR |
hitrank |
an integer indicates how many peptides to retain for a spectrum. A spectrum can match to multiple peptides. Default is 1. |
minpeplen |
an integer of minimum peptide length |
decoyprefix |
a character indicates decoy sequence in the 'protein' column. Usually is 'rev_' or 'DECOY_'. |
... |
additional arguments |
Filter the peptide identification based on FDR, hit rank, or peptide length.
a data frame object, contain PSMs (peptide spectrum match) passed the filters.
Xiaojing Wang
##MyriMatch example pepxml <- system.file("extdata/pepxml", "Myrimatch.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) passed <- PSMfilter(tttt, pepFDR=0.01, scorecolumn='mvh', hitrank=1, minpeplen=6, decoyprefix='rev_')