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,
      protein_col = "ProteinName",
      peptide_col = c("Peptide.Sequence", "FullPeptideName"),
      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.
`protein_col` | Column with protein identifiers. Default: ProteinName
`peptide_col` | Column with peptide identifiers. Default: Peptide.Sequence or FullPeptideName
`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, Peter Blattmann

### 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 1.24.0 Index]