checkgDNAstart {HLAtools}

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.