R/IMGT_Parse.R

In victoraLab/clonality: Easily Define Groups Of T/B Cells

#' Annotate clonality
#'
#' Returns the input table with the clonality annotations.
#'
#' @param data A data frame object or the full path to a xlsx with repertoire data.

#' @export
#'
#'
#'

#IMGT Summary file header
imgt.header <- c("Sequence number","Sequence ID","V-DOMAIN Functionality","V-GENE and allele","V-REGION score","V-REGION identity %","V-REGION identity nt","V-REGION identity % (with ins/del events)","V-REGION identity nt (with ins/del events)","J-GENE and allele","J-REGION score","J-REGION identity %","J-REGION identity nt","D-GENE and allele","D-REGION reading frame","CDR1-IMGT length","CDR2-IMGT length","CDR3-IMGT length","CDR-IMGT lengths","FR-IMGT lengths","AA JUNCTION","JUNCTION frame","Orientation","V-DOMAIN Functionality comment","V-REGION potential ins/del","J-GENE and allele comment","V-REGION insertions","V-REGION deletions","Sequence","5prime trimmed-n nb","3prime trimmed-n nb","Analysed sequence length","Sequence analysis category")

imgt.header