Filter OpenSWATH output table according to mscore and conditions.

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).

filter_mscore_condition(
  data,
  mscore,
  n_replica,
  peptide_col = c("Peptide.Sequence", "FullPeptideName"),
  charge_col = "Charge",
  condition_col = "Condition",
  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.

n_replica

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

peptide_col

Column with peptide identifiers. Default: Peptide.Sequence or FullPeptideName

charge_col

Column with peptide charge. Default: Charge

condition_col

Column with conditions. Default: Condition

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

Data which has been filtered.

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