filter_mscore {SWATH2stats}R Documentation

filter_mscore: Filter openSWATH output table according to mscore

Description

This function filters the SWATH data according to the 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)
filter_mscore_freqobs(data, mscore, percentage=NULL, rm.decoy = TRUE)
filter_mscore_condition(data, mscore, n.replica, rm.decoy = TRUE)

Arguments

data

A data frame containing SWATH data.

mscore

Value that defines the mscore threshold according to which the data will be filtered.

n.replica

Number of measurements within at least one condition that have to pass the mscore threshold for this transition.

percentage

Percentage in which replicas the transition has to reach the mscore threshold

rm.decoy

Option to remove the decoys during filtering.

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)


[Package SWATH2stats version 1.12.1 Index]