checkgDNAstart: Identify gDNA Alignments in Which the First Feature Boundary...

In HLAtools: Toolkit for HLA Immunogenomics

Identify gDNA Alignments in Which the First Feature Boundary is not Identified as Position +1.

Description

Checks the position of the first feature boundary (the 5' UTR - Exon 1 boundary in expressed genes) in each gDNA alignment, and identifies those alignments in which that position is not 1.

Usage

checkgDNAstart(verbose = FALSE)

Arguments

verbose

A logical indicating if loci with first feature boundary positions that are not 1 should be reported in the console (verbose = TRUE).

Details

This function reviews the gDNA atlases in the HLAatlas object and returns a data frame of the first feature boundary position for each locus. For expressed genes and some pseudogenes, this is the position of the start of Exon 1.

Value

A one-row data frame with one column for each locus with a gDNA alignment.

Note

This function requires that the HLAalignments object has been populated with alignments via the alignmentFull() function.

For internal HLAtools use.

HLAtools documentation built on June 8, 2025, 12:24 p.m.