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

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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.

Value

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

Author(s)

Moritz Heusel

Examples

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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)

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