write_matrix_peptides {SWATH2stats} | R Documentation

## Writes out an overview matrix of peptides mapping to a FDR quality controlled protein master list at controlled global peptide FDR quality.

### Description

Writes out an overview matrix on peptide level of a supplied (unfiltered or prefiltered) OpenSWATH results data frame. The peptide quantification is achieved by summing the areas under all 6 transitions per precursor and summing all precursors per FullPeptideName. In order to keep the peptide-to-protein association, the FullPeptideName is joined with the ProteinName.

### Usage

    write_matrix_peptides(
      data,
      write_csv = FALSE,
      fun_aggregate = "sum",
      filename = "SWATH2stats_overview_matrix_peptidelevel.csv",
      rm_decoy = FALSE
    )

### Arguments

`data` | A data frame containing annotated OpenSWATH/pyProphet data.
`write_csv` | Option to determine if table should be written automatically into csv file.
`fun_aggregate` | What function to use when aggregating the set of intensities (sum or mean)?. Default: sum.
`filename` | File base name of the .csv matrix written out to the working folder.
`rm_decoy` | Logical whether decoys will be removed from the data matrix. Defaults to FALSE. It's sometimes useful to know how decoys behave across a dataset and how many you allow into your final table with the current filtering strategy.

### Value

the peptides as a matrix! also output .csv matrix is written to the working folder.

### Author(s)

Moritz Heusel

### Examples

    {
     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- sample_annotation(OpenSWATH_data, Study_design)
     written <- write_matrix_peptides(data)
     }

[Package SWATH2stats version 1.20.1 Index]