filter_on_max_peptides: Filter only for the highest intense peptides

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

Filter only for the highest intense peptides

Description

In order to reduce the data, the data is filtered only for the proteins with the highest intensity peptides.

Usage

filter_on_max_peptides(
  data,
  n_peptides,
  protein_col = "ProteinName",
  peptide_col = c("Peptide.Sequence", "FullPeptideName"),
  rm.decoy = TRUE
)

Arguments

data	A data frame containing SWATH data with the column names: ProteinNames, PeptideSequence, PrecursorCharge, Intensity.
n_peptides	Maximum number of highest intense peptides to filter the data on.
protein_col	Column with protein identifiers. Default: ProteinName
peptide_col	Column with peptide identifiers. Default: Peptide.Sequence or FullPeptideName
rm.decoy	Option to remove the decoys during filtering.

Value

Returns a data frame of the filtered data.

Author(s)

Peter Blattmann

Examples

{
 data("OpenSWATH_data", package="SWATH2stats")
 data("Study_design", package="SWATH2stats")
 data <- sample_annotation(OpenSWATH_data, Study_design)
 data.filtered <- filter_mscore_freqobs(data, 0.01,0.8)
 data.max <- filter_on_max_peptides(data.filtered, 5)
 }

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