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

Description Usage Arguments Value Author(s) Examples

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

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

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)


Search within the SWATH2stats package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.