filter_on_max_peptides: Filter only for the highest intense peptides
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

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

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

`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.

Returns a data frame of the filtered data.

Peter Blattmann

{
 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)
 }