getNarrowCDNA: Give 'narrow' cDNA sequence of gene conversion events in the...

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

Give 'narrow' cDNA sequence of gene conversion events in the observed and the germline sequences.

Description

Give 'narrow' cDNA sequence of gene conversion events in the observed and the germline sequences.

Usage

getNarrowCDNA(start, end, start_c, end_c, seq_id, repertoire, seq)

Arguments

start	numeric, start point of gene conversion event. (column start from output of batchConvertAnalysis)
end	numeric, end point of gene conversion event. (column start from output of batchConvertAnalysis)
start_c	numeric, position in the codon (i.e. 1, 2, or 3) for the start point of gene conversion event.
end_c	numeric, position in the codon (i.e. 1, 2, or 3) for the end point of gene conversion event.
seq_id	character, identifier for the sequence of interest. i.e. the relevant entry in the SeqID column of the 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.
seq	character, an ungapped DNA sequence of the functional allele.

Value

A vector with two characters. The first item corresponds to the cDNA sequence corresponding to the location of the annotated gene conversion event, taken from functional. The second item corresponds to the cDNA sequence at the location of the gene conversion event, observed for the given seq_id in repertoire.

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