The function is written to take input from one protein at a time and requires three inputs: protein_sig, pi_not and max_proteforms
bpquant_mod(protein_sig, pi_not, max_proteoforms)is a matrix or data.frame with p rows and n columns, where p is the number of peptides mapped to the protein of interest and n is the number of tests conducted to generate signatures made up of values 0, 1, and -1.
is a numeric value between 0 and 1 indicating the background probability/frequency of a zero signature.
a numeric value, a maximum threshold for the number of possible proteoforms.
a list of five items: num_proteoforms, unique_sigs, proteoform_configs, post_prob and peptide_idx
| num_proteoforms | the number of proteoforms as identified by bpquant |
| unique_sigs | matrix of unique signatures observed |
| proteoform_configs | matrix of 0/1 values indicating scenarios of proteoform absence/presence scenarios |
| post_prob | vector of posterior probabilities corresponding to each proteoform configuration in "proteoform_configs" |
| peptide_idx | vector of 0, 1, 2, . . . values indicating which proteoform each peptide belongs to |