assess_decoy_rate {SWATH2stats} | R Documentation |
This function assesses the number of quantifications (typically peptides) that are decoys (false-positive) versus true identifications.
assess_decoy_rate(data, column = "FullPeptideName", column_decoy = "decoy")
data |
A data frame that contains at least a column named "FullPeptideName" and "decoy". |
column |
The column name of the Peptide identifier. Default: FullPeptideName. |
column_decoy |
The column name of the decoy column. Default: decoy. |
A printout is generated to indicate the number of non-decoy, decoy peptides and the rate of decoy vs non-decoy peptides. Unique peptides are counted, so a precursor with different charge states is counted as one peptide. In the column "decoy" the values need to be 1,0 or TRUE and FALSE.
Message detailing the number of decoys, non-decoys, and the ratio.
Peter Blattmann
data("OpenSWATH_data", package="SWATH2stats") data <- OpenSWATH_data assess_decoy_rate(data)