T.goodness.test: Test of fit of clonal deconvolution

In Subhayan18/CRUST: Multi-regional clonal deconvolution of tumor sequencing data

Description

A chi square test to assess the goodness of fit of the clonal : sub-clonal clouds. This test can be used to obtain outliers that do not fit into the proposed clonal deconvolution space.

Usage

T.goodness.test(x)

Arguments

x	A dataframe with the first three columns in the specific order: sample name or ID of a variant, variant allele frquencies (VAF) and cancer cell fraction (CCF)

Value

A list of two objects. x is same as the input dataframe with addede columns named expected VAF_, chi_sq_ and P value_ corresponding to each cloud of clone : Sub-clone combination. rej is a subset of x containing variants that fail the test for at least one cloud.

expected VAF_ represents estimated variant allele frequencies for a given cloud.

chi_sq_ is the Chi square test statistic for the cloud.

P value_ is the P value corresponding to the chi_sq_ statistic.

Examples

#test<-T.goodness.test(test.dat)
#head(test)

Subhayan18/CRUST documentation built on Dec. 18, 2021, 3:03 p.m.