adjustBroadPos: Give 'broad' start/end points of gene conversion events

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

Give 'broad' start/end points of gene conversion events

Description

This function gives the 'broad' definition of gene conversion event boundaries, i.e. the start/end coordinates given in batchConvertAnalysis with added nucleotides corresponding to sequence stretches 5'/3' of start/end points identical between the observed repertoire sequence and the pseudogene. The output respects the same numbering scheme, respecting the imposed gaps ('.') in the input repertoire.

Usage

adjustBroadPos(tb, repertoire)

Arguments

tb	data.frame, output from batchConvertAnalysis.
repertoire	A named vector of strings storing nucleotide sequences observed from a repertoire. The names attribute of the vector stores the sequence identifiers.

Value

A data.frame with these two columns added to tb:

soft_start

the position given in the start column, padded with the number of nucleotides given in fiveprime_identical_length.

soft_end

the position given in the end column, padded with the number of nucleotides given in threeprime_identical_length.

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