filter_on_min_peptides: Filter openSWATH output for proteins that are identified by a...

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

Filter openSWATH output for proteins that are identified by a minimum of n independent peptides.

Description

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.

Usage

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

Arguments

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.

Value

Returns the filtered data frame with only peptides that map to proteins with >= n_peptides peptides.

Author(s)

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

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