testNeutral: testNeutral

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

Evaluate whether a tumor follows neutral evolution or under strong selection during the growth based on variant frequency distribution (VAF) of subclonal mutations. The subclonal mutant allele frequencies of a follow a simple power-law distribution predicted by neutral growth.

Usage

testNeutral(
  maf,
  patient.id = NULL,
  withinTumor = FALSE,
  min.total.depth = 2,
  min.vaf = 0.1,
  max.vaf = 0.3,
  R2.threshold = 0.98,
  min.mut.count = 20,
  plot = TRUE,
  use.tumorSampleLabel = FALSE,
  ...
)

Arguments

maf	Maf or MafList object generated by readMaf function.
patient.id	Select the specific patients. Default NULL, all patients are included.
withinTumor	Test neutral within tumros in each patients. Default FALSE.
min.total.depth	The minimun total depth of coverage. Defalut 2
min.vaf	The minimum value of adjusted VAF value. Default 0.1
max.vaf	The maximum value of adjusted VAF value. Default 0.3
R2.threshold	The threshod of R2 to decide whether a tumor follows neutral evolution. Default 0.98
min.mut.count	The minimun number of subclonal mutations used to fit model. Default 20
plot	Logical, whether to print model fitting plot of each sample. Default TRUE.
use.tumorSampleLabel	Let Tumor_Sample_Barcode replace Tumor_Sample_Label if Tumor Label is provided in clinical data. Default FALSE.
...	Other options passed to subMaf

Value

the neutrality metrics and model fitting plots

References

Williams, M., Werner, B. et al. Identification of neutral tumor evolution across cancer types. Nat Genet 48, 238-244 (2016)

Examples

maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit")
clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit")
ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit")
maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19")
testNeutral(maf)

MesKit documentation built on March 28, 2021, 6 p.m.