filter_mscore_freqobs: Filter OpenSWATH output table according to mscore.

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description

This function filters the SWATH data according to the m_score value, as well as to the number of occurence in the data.

Usage

filter_mscore_freqobs(
  data,
  mscore,
  percentage = NULL,
  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.
percentage	Percentage in which replicas the transition has to reach the mscore threshold.
rm.decoy	Option to remove the decoys during filtering.
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.