filter_all_peptides {SWATH2stats} | R Documentation

## Select all proteins that are supported by peptides.

### Description

This function can be used as opposed to the function "filter_proteotypic_peptides()". This function counts all proteins (including proteins supported by non proteo-typic (i.e. shared) peptides). All peptides (incl. non proteotypic peptides are selected. For the proteins supported by proteotypic peptide the "1/" in front of the identifier is removed to facilitate further data processing. The protein identifier of shared peptides needs to be separated by a slash "/".

### Usage

    filter_all_peptides(data)

### Arguments

`data` | A data frame containing SWATH data.

### Value

Returns a data frame with the data from both proteotypic and non-proteotypic peptides.

### Author(s)

Peter Blattmann

### Examples

    {
     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- sample_annotation(OpenSWATH_data, Study_design)
     data.filtered.decoy <- filter_mscore(data, 0.01)
     data.all <- filter_all_peptides(data.filtered.decoy)
     }

[Package SWATH2stats version 1.20.1 Index]