filter_mscore {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(data, mscore, rm.decoy=TRUE, mscore.col = "m_score") filter_mscore_freqobs(data, mscore, percentage=NULL, rm.decoy = TRUE, mscore.col = "m_score") filter_mscore_condition(data, mscore, n.replica, 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. |
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. |
Returns a data frame with the filtered data.
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)