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clonevol (version 0.99.11)

subclonal.test: Subclonal test of H0:

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