write_matrix_peptides: Writes out an overview matrix of peptides mapping to a FDR...
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

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.

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

`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.

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

Moritz Heusel

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