hla_read_alignment: Process HLA alignment data in *.nuc or *.gen files and return...

In genevol-usp/hlaseqlib: R utility functions for the HLA RNAseq project

Process HLA alignment data in *.nuc or *.gen files and return a data.frame.

Description

Process HLA alignment data in *.nuc or *.gen files and return a data.frame.

Usage

hla_read_alignment(locus, imgtdb, imgtfile = c("nuc", "gen"),
  exons = NULL, by_exon = FALSE, keep_sep = FALSE)

Arguments

locus	character string. The HLA locus to be processed (e.g., "A", "DRB1").
imgtdb	character string. Path to the IMGTHLA directory.
imgtfile	character string. Whether to process "nuc" or "gen" files.
exons	integer. Range of exons/introns (default is all exons/introns).
by_exon	logical. Whether to return sequences separated for each exon/intron (default FALSE).
keep_sep	logical. Whether to keep '|' as the separator between exons/introns.

Value

A data.frame.

Examples

## Not run: 
hla_read_alignment(locus = "DRB1", imgtdb = "~/IMGTHLA") 

## End(Not run)
## Not run: 
hla_read_alignment(locus = "A", imgtdb = "~/IMGTHLA", exons = c(2, 3))

## End(Not run)

genevol-usp/hlaseqlib documentation built on Aug. 24, 2022, 7:24 a.m.