vaf: Utilities for variant allele frequency

In heavywatal/rtumopp: R interface to tumopp, a tumor growth simulator in C++

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.