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

Description Usage Arguments Value Author(s) Examples

View source: R/filter_on_min_peptides.R

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

1
filter_on_min_peptides(data, n_peptides, 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.

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

Examples

1
2
3
4
5
6
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)

SWATH2stats documentation built on Nov. 17, 2017, 9:10 a.m.