doBlat: Extract sequence stretches to be analysed using BLAT.

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

Extract sequence stretches to be analysed using BLAT.

Description

Extract sequence stretches to be analysed using BLAT.

Usage

doBlat(seqname, repertoire, functional, gapwidth = 3, flank = 6)

Arguments

seqname	character, name of sequence in repertoire.
repertoire	a named vector of full-length sequences to be analysed. The names attribute of this vector stores the sequence identifiers.
functional	DNAStringSet object storing DNA sequences of the functional V gene alleles.
gapwidth	integer, the distance between separate mismatches to be grouped together as a 'gap' to be analysed as candidate gene conversion events. (default: 3)
flank	integer, the number of nucleotides to be included in the 'gap' sequences to be searched using BLAT to annotate for candidate gene conversion events. (default: 6)

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