filter_on_max_peptides {SWATH2stats} | R Documentation |
In order to reduce the data, the data is filtered only for the proteins with the highest intensity peptides.
filter_on_max_peptides( data, n_peptides, protein_col = "ProteinName", peptide_col = c("Peptide.Sequence", "FullPeptideName"), rm.decoy = TRUE )
data |
A data frame containing SWATH data with the column names: ProteinNames, PeptideSequence, PrecursorCharge, Intensity. |
n_peptides |
Maximum number of highest intense peptides to filter the data on. |
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 a data frame of 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_freqobs(data, 0.01,0.8) data.max <- filter_on_max_peptides(data.filtered, 5) }