neoCN: Find paired neo C-terminal neo N-terminal peptides

In tobiasko/posprot: Positional Proteomics in R

Description

This function looks for adjacent peptides (peptides being positioned head-to-tail at zero distance) taking the specificity of the test protease and the working protease into account. The function also checks for the presence of N-terminal labels on the peptides. These indicate that a peptide lies downstream of a cleavage site. Pairs of adjacent peptides, passing all specificity checks, are unified and returned as a single IRange.

Usage

neoCN(x, united = TRUE)

Arguments

x	IRanges object
united	Pairs object

Details

—XXXXX.XXXXX— ==> —XXXXXXXXXX—

This function expects test.prot.spec and work.prot.spec to be present in the environment.

Value

Function returns an IRanges object by default. If united is set to FALSE a pairs object returned.

tobiasko/posprot documentation built on May 26, 2019, 5:33 a.m.