Filter OpenSWATH output table according to mscore.

Source: R/filter_mscore_freqobs.R

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

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

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)
#> Dimension difference: 931, 0
 data.filtered <- filter_mscore_freqobs(data, 0.01, 0.8)
#> Treshold, peptides need to have been quantified in more conditions than: 4.8
#> Fraction of peptides selected: 0.42
#> Dimension difference: 1323, 0
 data.filtered <- filter_mscore_condition(data, 0.01, 3)
#> Fraction of peptides selected: 0.47
#> Dimension difference: 1209, 0