PSMfilter: Filter the peptide indentification.

In pepXMLTab: Parsing pepXML files and filter based on peptide FDR.

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

Details

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

Value

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

Author(s)

Xiaojing Wang

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_')

pepXMLTab documentation built on Nov. 8, 2020, 5:01 p.m.