write_matrix_peptides: Writes out an overview matrix of peptides mapping to a FDR...

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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)
 }

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.