filter_mscore: Filter OpenSWATH output table based on mscore.

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description

This function filters the SWATH/DIA data according to a m_score value, as well as to the number of occurence in the data (requant) and within a condition (condition).

Usage

filter_mscore(data, mscore, rm.decoy = TRUE, mscore.col = "m_score")

Arguments

data	A data frame containing SWATH data.
mscore	Value that defines the mscore threshold according to which the data will be filtered.
rm.decoy	Option to drop decoys from the data
mscore.col	Defines the column from which to retrieve the m_score. If you use JPP (Rosenberger, Bludau et al. 2017) this can be used to select between Protein and transition_group m_score.

Value

Returns a data frame with the filtered data

Author(s)

Peter Blattmann

Examples

 data("OpenSWATH_data", package="SWATH2stats")
 data("Study_design", package="SWATH2stats")
 data <- sample_annotation(OpenSWATH_data, Study_design)
 data.filtered <- filter_mscore(data, 0.01)
 data.filtered <- filter_mscore_freqobs(data, 0.01, 0.8)
 data.filtered <- filter_mscore_condition(data, 0.01, 3)

SWATH2stats documentation built on April 17, 2021, 6:01 p.m.