filter_on_min_peptides {SWATH2stats} | R Documentation |
This function removes entries mapping to proteins that are identified by less than n_peptides. Removing single-hit proteins from an analysis can significantly increase the sensitivity under strict protein fdr criteria, as evaluated by e.g. assess_fdr_overall.
filter_on_min_peptides( data, n_peptides, protein_col = "ProteinName", peptide_col = c("Peptide.Sequence", "FullPeptideName"), rm.decoy = TRUE )
data |
Data table that is produced by the OpenSWATH/iPortal workflow. |
n_peptides |
Number of minimal number of peptide IDs associated with a protein ID in order to be kept in the dataset. |
protein_col |
Column with protein identifiers. Default: ProteinName |
peptide_col |
Column with peptide identifiers. Default: Peptide.Sequence or FullPeptideName |
rm.decoy |
Option to remove the decoys during filtering. |
Returns the filtered data frame with only peptides that map to proteins with >= n_peptides peptides.
Moritz Heusel, Peter Blattmann
{ data("OpenSWATH_data", package="SWATH2stats") data("Study_design", package="SWATH2stats") data <- sample_annotation(OpenSWATH_data, Study_design) data.filtered <- filter_mscore_freqobs(data, 0.01,0.8) data.max <- filter_on_max_peptides(data.filtered, 5) data.min.max <- filter_on_min_peptides(data.max, 3) }