write_matrix_peptides {SWATH2stats} | R Documentation |
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) }