vaf: Utilities for variant allele frequency

make_vafR Documentation

Utilities for variant allele frequency

Description

Utilities for variant allele frequency

Usage

make_vaf(graph, samples, mu, accel = 0)

make_longer_vaf(graph, samples, mu, threshold = 0.05)

longer_vaf(vaf)

filter_detectable(vaf, threshold)

sort_vaf(vaf, method = c("average", "ward.D2", "complete", "single"))

Arguments

graph

igraph

samples

list of integer IDs

mu

mutation rate per cell division (ignored if segsites is given)

accel

assumption undocumented yet

threshold

minimum detectable frequency

vaf

output of make_vaf()

method

passed to stats::hclust

Details

make_vaf generates neutral VAF pattern from cell genealogy.

make_longer_vaf is a shortcut to make VAF in longer format.

longer_vaf transforms vaf table.

filter_detectable removes sites where freq < threshold.

sort_vaf reorders rows and columns of VAF table.


heavywatal/rtumopp documentation built on Aug. 27, 2024, 11:50 a.m.