bpquant_mod {pmartR}

bpquant_mod function

Description

The function is written to take input from one protein at a time and requires three inputs: protein_sig, pi_not and max_proteforms

Usage

bpquant_mod(protein_sig, pi_not, max_proteoforms)

Arguments

protein_sig

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.

pi_not

is a numeric value between 0 and 1 indicating the background probability/frequency of a zero signature.

max_proteoforms

a numeric value, a maximum threshold for the number of possible proteoforms.

Details

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

Value

a list of five items: num_proteoforms, unique_sigs, proteoform_configs, post_prob and peptide_idx