filter_on_min_peptides {SWATH2stats} | R Documentation

## Filter openSWATH output for proteins that are identified by a minimum of n independent peptides

### Description

This function removes entries mapping to proteins that are identified by less than n_peptides.

Removing single-hit proteins from an analysis can significantly increase the sensitivity under strict protein fdr criteria, as evaluated by e.g. assess_fdr_overall.

### Usage

    filter_on_min_peptides(data, n_peptides, rm.decoy = TRUE)

### Arguments

`data` | Data table that is produced by the openSWATH/iPortal workflow.
`n_peptides` | Number of minimal number of peptide IDs associated with a protein ID in order to be kept in the dataset.
`rm.decoy` | Option to remove the decoys during filtering.

### Value

Returns the filtered data frame with only peptides that map to proteins with >= n_peptides peptides.

### Author(s)

Moritz Heusel

### Examples

    data("OpenSWATH_data", package="SWATH2stats")
    data("Study_design", package="SWATH2stats")
    data <- sample_annotation(OpenSWATH_data, Study_design)
    data.filtered <- filter_mscore_freqobs(data, 0.01,0.8)
    data.max <- filter_on_max_peptides(data.filtered, 5)
    data.min.max <- filter_on_min_peptides(data.max, 3)

[Package SWATH2stats version 1.18.0 Index]