getAAGeneConversion: Translate amino acid sequences for gene conversion events

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

Translate amino acid sequences for gene conversion events

Description

Translate amino acid sequences for gene conversion events

Usage

getAAGeneConversion(tb, repertoire, functional)

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.
functional	character, filepath to FASTA file containing DNA sequence(s) of the functional V gene allele(s).

Value

A data.frame with these columns added to tb:

germline_AA_narrow

(Amino acid sequence of the region between start and end, from the functional germline allele.

observed_AA_narrow

Amino acid sequence of the region between start and end, from the observed sequence sampled in the repertoire data.

germline_AA_broad

Amino acid sequence of the region between start and end plus the flanking stretches given by fiveprime_identical_length and threeprime_identical_length, from the functional germline allele.

observed_AA_broad

(Amino acid sequence of the region between start and end plus the flanking stretches given by fiveprime_identical_length and threeprime_identical_length, from the observed sequence sampled in the repertoire data.

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