get_IBS_distance: Get identity by state (IBS) distance

In mrc-ide/MIPanalyzer: Filtering and analysis of MIP data

Get identity by state (IBS) distance

Description

Get identity by state (IBS) distance, computed as the proportion of sites that are identical between samples. If ignore_het = TRUE then heterozygous sites are ignored, otherwise the major strain is called at every locus.

Usage

get_IBS_distance(x, ignore_het = TRUE, diagonal = NULL, report_progress = TRUE)

Arguments

x	object of class mipanalyzer_biallelic.
ignore_het	whether to ignore heterozygous comparisons, or alternatively call the major allele at every locus (see details).
diagonal	Should the diagonal of the distance matrix be changed to a given value. Default = NULL, which cause no changes.
report_progress	if TRUE then a progress bar is printed to the console.

mrc-ide/MIPanalyzer documentation built on Jan. 17, 2024, 7:16 p.m.