ScanGeneConversion: Wrapper function to scan and annotate gene conversion events

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

Wrapper function to scan and annotate gene conversion events

Description

Wrapper function to scan and annotate gene conversion events

Usage

ScanGeneConversion(
  seqname,
  repertoire,
  functional,
  pseudogenes,
  blat_all,
  blat_whole,
  lut,
  gapwidth = 3
)

Arguments

seqname	character, identifier of a given sequence from repertoire, for which gene conversion events are to be annotated.
repertoire	A named vector of strings storing nucleotide sequences observed from a repertoire. The names attribute of the vector stores the sequence identifiers.
functional	DNAStringSet object storing nucleotide sequences of the functional alleles of the V gene.
pseudogenes	DNAStringSet object storing nucleotide sequences of the pseudogene alleles of the V gene.
blat_all	data.frame storing BLAT results when searching subsequences taken from repertoire against the pseudogene sequences.
blat_whole	data.frame storing BLAT results when searching the full-length repertoire sequences against the pseudogene sequences. This is used to supplement pseudogene matches given in blat_all
lut	A IRanges object storing positions of mismatches comparing all functional alleles against all pseudogene alleles.
gapwidth	integer, the number of nucleotides that separate mismatches to be grouped together as one candidate gene conversion event.

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