attach_imgt_alleles: Find best matching IMGT reference alleles for TCR V and J...

In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq

Find best matching IMGT reference alleles for TCR V and J gene segments

Description

Entries from seq are made unique and are matched against reference alleles in imgt_ref. If names are provided to seq (or respective V and J columns in case of a data frame) matching will be quicker as possibles alleles are initially narrowed down by string matching.

Usage

attach_imgt_alleles(
  seq,
  imgt_ref,
  pick.by = "alignment",
  lapply_fun = lapply,
  seq_col = "consensus_seq_cr",
  V_col = "V_cr",
  J_col = "J_cr",
  ...
)

Arguments

seq	data frame with clonotype data in long format, e.g. cl_long preferentially from igsc::read_cellranger_outs or a named vector of consensus sequences, named by V and J segments, separated by ""; e.g. stats::setNames(object = cl_long$consensus_seq_cr, nm = paste0(cl_long$V_cr, '', cl_long$J_cr))
imgt_ref	IMGT reference data frame created with igsc::imgt_tcr_segment_prep or a named vector of sequences and respective allele names; e.g. stats::setNames(imgt_ref$seq.nt, imgt_ref$Allele)
pick.by	match disambiguate alleles from IMGT by best match (alignment) or just randomly (random); random is intended to speed up the process for testing or when exact IMGT alleles are not necessary
lapply_fun	function name without quotes; lapply, pbapply::pblapply or parallel::mclapply are suggested
...	additional argument to the lapply function; mainly mc.cores when parallel::mclapply is chosen

Value

a data frame of unique seq entries in column

Examples

## Not run: 
imgt_ref <- readRDS(system.file("extdata", "IMGT_ref/human/hs.rds", package = "igsc"))
ata <- attach_imgt_alleles(seq = cl_long, imgt_ref = imgt_ref, pick.by = "random", lapply_fun = lapply)
cl_long <-
dplyr::left_join(cl_long, ata, by = c("consensus_seq_cr" = "seq")) %>%
tidyr::separate(VJ_IMGT, into = c("V_imgt", "J_imgt"), sep = "___")

## or pass vector, named or unnamed
ata <- attach_imgt_alleles(seq = cl_long$consensus_seq_cr, imgt_ref = imgt_ref, pick.by = "random", lapply_fun = lapply)

ata <- attach_imgt_alleles(seq = stats::setNames(object = cl_long$consensus_seq_cr, nm = paste0(cl_long$V_cr, '___', cl_long$J_cr)),
imgt_ref = imgt_ref, pick.by = "random", lapply_fun = lapply)

## End(Not run)

Close-your-eyes/igsc documentation built on Jan. 28, 2024, 10:28 p.m.