getBroadCDNA: Give 'broad' cDNA sequence of gene conversion events in the...

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

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

Description

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

Usage

getBroadCDNA(
  soft_start,
  start,
  soft_end,
  end,
  start_c,
  end_c,
  seq_id,
  repertoire,
  seq
)

Arguments

soft_start	numeric, start point of gene conversion event padded with the 5' identical sequence stretch. (column soft_start from the output of adjustBroadPos.)
start	numeric, start point of gene conversion event. (column start from output of adjustBroadPos)
soft_end	numeric, end point of gene conversion event padded with the 3' identical sequence stretch. (column soft_end from the output of adjustBroadPos.)
end	numeric, end point of gene conversion event. (column start from output of adjustBroadPos)
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 adjustBroadPos.
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 'broad' definition of the annotated gene conversion event, taken from functional. The second item corresponds to the cDNA sequence for the 'broad' definition 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.