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).
filter_mscore(data, mscore, rm.decoy = TRUE, mscore.col = "m_score")A data frame containing SWATH data.
Value that defines the mscore threshold according to which the data will be filtered.
Option to drop decoys from the data
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.
Returns a data frame with the filtered data
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