pepXMLTab (version 1.6.0)

PSMfilter: Filter the peptide indentification.

Description

The PSMfilter() function filter the peptide identification based on user chosen paramter.

Usage

PSMfilter(PSMtab, pepFDR = 0.01, scorecolumn = "mvh", hitrank = 1, minpeplen = 6, decoyprefix = "rev_", ...)

Arguments

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

Value

a data frame object, contain PSMs (peptide spectrum match) passed the filters.

Details

Filter the peptide identification based on FDR, hit rank, or peptide length.

Examples

##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_')