filter_proteotypic_peptides {SWATH2stats} | R Documentation

## Filter for proteins that are supported by proteotypic peptides.

### Description

Peptides can match to several proteins. With this function proteotypic peptides, peptides that are only contained in one protein are selected. Additionally the number of proteins are counted and printed.

### Usage

    filter_proteotypic_peptides(data, rm.decoy = TRUE)

### Arguments

`data` | A data frame containing SWATH data.
`rm.decoy` | Option to remove the decoys during filtering.

### Value

Returns a data frame with only the data supported by 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_proteotypic_peptides(data.filtered.decoy)

[Package SWATH2stats version 1.14.0 Index]