subclonal.test: Subclonal test of H0:

In hdng/clonevol: Clonal ordering and visualization

Description

Return a list of p-value, confidence intervals of X-(X1+X2),etc. if p-value is small, reject H0, otherwise, not enough evidence to reject H0

Usage

subclonal.test(vaf.col.name, parent.cluster, sub.clusters = NULL,
  boot = NULL, cdf = NULL, min.cluster.vaf = 0, alpha = 0.05,
  alternative = "greater")

Arguments

boot:	output of generate.boot(), if NULL, test using VAFs
vaf.col.name:	name of the VAF column
parent.cluster:	the cluster of mutations representing the parent clone
sub.clusters:	vector of sub clusters to test if they can be all directly arise from the parent clone; if NULL, the parent.cluster will be tested against 0 (this will help determine if this (parent)clone represents with high enough cell frac to report)
cdf:	Clonal data frame with VAF
min.cluster.vaf:	if not NULL and no bootstrap used, any cluster VAF smaller than this is considered zero
alternative:	alternative hypothesis c('greater', 'less') default = 'greater' ie. Ha: mean_X >= mean_X1 + mean_X2

hdng/clonevol documentation built on May 17, 2019, 3:19 p.m.