filter_mscore_condition {SWATH2stats} | R Documentation |
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" )
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. |
Data which has been filtered.
Peter Blattmann
{ 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) }