mergeHits: Function to merge adjacent events explainable by the same...

In Fraternalilab/BrepConvert: BrepConvert: R package for gene conversion analysis of B cell repertoire

Function to merge adjacent events explainable by the same donor pseudogene

Description

This function merges adjacent events only if the intervening sequence stretch is COMPLETELY identical between the functional allele and the nominated donor pseudogene. As a result of the merge, the boundaries, edit distance and other annotations of the events are adjusted accordingly.

Usage

mergeHits(hits, lut_functional)

Arguments

hits	data.frame storing annotations of the nominated hits (donor pseudogenes) that explain all gene conversion event generated by running the BLAT program.
lut_functional	an IRanges object storing positions of mismatches between all functional alleles against all pseudogene alleles. This acts as a lookup table to determine whether the functional allele and any given pseudogene share identical nucleotide sequences within a range of interest.

Fraternalilab/BrepConvert documentation built on Oct. 14, 2022, 5:54 p.m.