neutralitytestr (version 0.0.3)

neutralitytest: Testing for neutrality on cancer sequencing data

Description

neutralitytest returns a neutralitytest object which contains the result of various test statistics to test for neutrality as described in Williams et al. Nature Genetics 2018. WARNING: This package has been superseded by MOBSTER, see Caravagna et al. Nature Genetics 2020.

Usage

neutralitytest(
  VAF,
  fmin = 0.1,
  fmax = 0.25,
  read_depth = NULL,
  rho = 0,
  cellularity = 1,
  ploidy = 2
)

Arguments

VAF

Vector of variant allele frequencies (VAFs) from a deep sequencing experiment, numbers should be between 0 and 1

fmin

Minimum VAF of integration range, default is 0.1

fmax

Maximum VAF of integration range, default is 0.25

read_depth

Read depth of sample, if this is specified it will be used to calculate an approptiate integration range. default is NULL in which case the default or inputted fmin and fmax will be used.

rho

Overdispersion of sample if known, default is 0.0. Will be used to calculate integration range if read_depth != NULL

cellularity

Cellularity of sample, default is 1.0. Will be used to calculate integration range if read_depth != NULL

ploidy

Ploidy of the genome, default is 2. Ideally mutations should be filtered for this ploidy before running the test. Will be used to calculate integration range if read_depth != NULL

Value

neutralitytest object which contains test statistics which tests if the sequencing data is consistent a neutral evolutionary model. Test statistics are area between theoretical and empirical curves, kolmogorov distance, mean distance and R^2 statistics from linear model fit. Also returns an estimate of the mutation rate per tumour tumour doubling, the raw VAFs and cumulative distribution

Examples

# NOT RUN {
neutralitytest(runif(100))
neutralitytest(VAFselection, fmin = 0.1, fmax = 0.25)
neutralitytest(VAFneutral, read_depth = 100.0, cellularity = 0.8)
# }