This function counts the number of peptides that map to each protein and/or the number of proteins to which each individual peptide maps.
proteomics_filter(omicsData)an object of class "pepData", the a result of
as.pepData or as.isobaricpepData. The e_meta
component of omicsData must be nonempty.
An S3 object of class proteomicsFilt, which is a list with two elements. The first element is a data frame of counts for each unique peptide. The second element is a data frame with the counts for the number of peptides that map to each unique protein.
library(pmartRdata)
my_filter <- proteomics_filter(omicsData = pep_object)
summary(my_filter, min_num_peps = 3)