filter_on_min_peptides: Filter openSWATH output for proteins that are identified by a...
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

This function removes entries mapping to proteins that are identified by less than n_peptides. Removing single-hit proteins from an analysis can significantly increase the sensitivity under strict protein fdr criteria, as evaluated by e.g. assess_fdr_overall.

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

`data`	Data table that is produced by the OpenSWATH/iPortal workflow.
`n_peptides`	Number of minimal number of peptide IDs associated with a protein ID in order to be kept in the dataset.
`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 the filtered data frame with only peptides that map to proteins with >= n_peptides peptides.

Moritz Heusel, 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)
 data.min.max <- filter_on_min_peptides(data.max, 3)
 }