filter_mscore: Filter OpenSWATH output table based on mscore.

Description Usage Arguments Value Author(s) Examples

View source: R/filter_mscore.R

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

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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

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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(data, 0.01)
 data.filtered <- filter_mscore_freqobs(data, 0.01, 0.8)
 data.filtered <- filter_mscore_condition(data, 0.01, 3)

peterblattmann/SWATH2stats documentation built on April 20, 2021, 12:02 p.m.