readGliph: Read GLIPH files

In shashidhar22/LymphoSeq2: 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 GLIPH2 files to match input TRB file names so that the GLIPH2 table and repertoire table can be merged

Details

The files contain three columns, the GLIPH2 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)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.