filter_on_max_peptides {SWATH2stats} | R Documentation

## Filter only for the highest intense peptides

### Description

In order to reduce the data, the data is filtered only for the proteins with the highest intensity peptides.

### Usage

    filter_on_max_peptides(
      data,
      n_peptides,
      protein_col = "ProteinName",
      peptide_col = c("Peptide.Sequence", "FullPeptideName"),
      rm.decoy = TRUE
    )

### Arguments

`data` | A data frame containing SWATH data with the column names: ProteinNames, PeptideSequence, PrecursorCharge, Intensity.
`n_peptides` | Maximum number of highest intense peptides to filter the data on.
`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 a data frame of the filtered data.

### Author(s)

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)
     }

[Package SWATH2stats version 1.20.1 Index]