pepXML2tab: Generate a data frame objects from a pepXML file.

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

Description

The pepXML2tab() function generates a data frame from a pepXML file.

Usage

pepXML2tab(pepxml, ...)

Arguments

pepxml	a character contains the path and name of a pepXML file
...	additional arguments

Details

Read peptide identification from pepXML file into an data frame object.

Value

a data frame object, each row represent a PSM (peptide spectrum match) from the pepXML file

Author(s)

Xiaojing Wang

Examples

## 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)

Example output

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