Get genomic distance between samples

Get genomic distance between samples using a distance metric that allows for mixed infections and takes account of linkage (see references for details).

get_genomic_distance(x, cutoff = 0.1, report_progress = TRUE)

Arguments

x

object of class mipanalyzer_biallelic.

cutoff

when calculating weights, correlations below this value are ignored (see references).

report_progress

if TRUE then a progress bar is printed to the console.

References

MalariaGEN Plasmodium falciparum Community Project. "Genomic epidemiology of artemisinin resistant malaria". eLIFE (2016).