SWATH2stats (version 1.2.3)

write_matrix_peptides: write_matrix_peptides: 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, 
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.

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

No return value, output .csv matrix is written to the working folder.

Examples

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