readGliph: Read GLIPH files

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

Read GLIPH files

Description

readGliph Imports tab-separated value (.tsv) files generated by GLIPH

Usage

readGliph(gliph_path)

Arguments

gliph_path

Path containing GLIPH convergence group files. The file name will be used as repertoire_id in the output, it is advisable to rename the GLIPH files to match input TRB file names so that the GLIPH table and repertoire table can be merged

Details

#' @details The files contain three columns, the gliph convergence group count, The specificity group sequence and a space separated list of junction_aa sequences. The function reads these files into a tibble with three columns, expanding the junction_aa column such that each row in the tibble corresponds to one junction_aa

Value

Tibble with four columns, repertoire_id, gliph count, specificity group and junction amino acid sequence. The GLIPH file name is used as the repertoire_id

Examples

file_path <- base::system.file("extdata", "TCRB_gliph", package = "LymphoSeq2") 
gliph_table <- LymphoSeq2::readGliph(file_path)

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.