filter_all_peptides {SWATH2stats} | R Documentation

## Select all proteins that are supported by peptides.

### Description

This functions counts all proteins that are supported by peptides (including non proteo-typic peptides). All peptides (incl. non proteotypic peptides are selected. For the proteins supproted by proteotypic peptide the "1/" in front of the identifier is removed to facilitate further data processing.

### 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 1.10.2 Index]