Provide summary of a proteomicsFilt S3 object
# S3 method for class 'proteomicsFilt'
summary(object, min_num_peps = NULL, degen_peps = FALSE, ...)S3 object of class 'proteomicsFilt' created by
proteomics_filter.
optional integer value between 1 and the maximum
number of peptides that map to a protein in the data. The value specifies
the minimum number of peptides that must map to a protein. Any protein with
less than min_num_peps mapping to it will be returned as a protein
that should be filtered. Default value is NULL.
logical indicator of whether to filter out 'degenerate' or 'redundant' peptides (i.e. peptides mapping to multiple proteins) (TRUE) or not (FALSE). Default value is FALSE.
further arguments passed to or from other methods
a summary table giving the number of Observed Proteins per Peptide and number of Observed Peptides per Protein. If min_num_peps is specified and/or degen_peps is TRUE, the number of biomolecules to be filtered with the specified threshold(s) are reported.
library(pmartRdata)
myfilt <- proteomics_filter(omicsData = pep_object)
summary(myfilt, degen_peps = TRUE) # there are no degenerate peptides to filter out
summary(myfilt, min_num_peps = 2)