| Title: | Parsing pepXML files and filter based on peptide FDR. |
|---|---|
| Description: | Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR. |
| Authors: | Xiaojing Wang |
| Maintainer: | Xiaojing Wang <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.39.0 |
| Built: | 2024-07-15 04:59:32 UTC |
| Source: | https://github.com/bioc/pepXMLTab |
The pepXML2tab() function generates a data frame from a pepXML file.
pepXML2tab(pepxml, ...)pepXML2tab(pepxml, ...)
pepxml |
a character contains the path and name of a pepXML file |
... |
additional arguments |
Read peptide identification from pepXML file into an data frame object.
a data frame object, each row represent a PSM (peptide spectrum match) from the pepXML file
Xiaojing Wang
## MyriMatch example pepxml <- system.file("extdata/pepxml", "Myrimatch.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) ## Mascot example pepxml <- system.file("extdata/pepxml", "Mascot.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) ## SEQUEST example pepxml <- system.file("extdata/pepxml", "SEQUEST.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) ## XTandem example pepxml <- system.file("extdata/pepxml", "XTandem.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml)## MyriMatch example pepxml <- system.file("extdata/pepxml", "Myrimatch.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) ## Mascot example pepxml <- system.file("extdata/pepxml", "Mascot.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) ## SEQUEST example pepxml <- system.file("extdata/pepxml", "SEQUEST.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml) ## XTandem example pepxml <- system.file("extdata/pepxml", "XTandem.pepXML", package="pepXMLTab") tttt <- pepXML2tab(pepxml)
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_", ...)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_')##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_')