calFst: calFst

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

Description

Genetic divergence between regions of subclonal sSNVs using the Weir and Cockerham method

Usage

calFst(
  maf,
  patient.id = NULL,
  min.vaf = 0,
  min.total.depth = 2,
  use.adjVAF = FALSE,
  plot = TRUE,
  withinTumor = FALSE,
  use.circle = TRUE,
  title = NULL,
  number.cex = 8,
  number.col = "#C77960",
  use.tumorSampleLabel = FALSE,
  ...
)

Arguments

maf	A Maf or MafList object generated by readMaf function.
patient.id	Select the specific patients. Default NULL, all patients are included.
min.vaf	Specify The minimum VAF to filter variants. Default 0.
min.total.depth	The minimum total allele depth for filtering variants. Default 2.
use.adjVAF	Use adjusted VAF in analysis when adjusted VAF or CCF is available. Default FALSE.
plot	Logical (Default: TRUE).
withinTumor	Logical (Default: FALSE). Whether calculate between-region heterogeneity within tumors.
use.circle	Logical (Default: TRUE). Whether use "circle" in the plot. as visualization method of correlation matrix
title	The title of the plot. Default "Nei's distance"
number.cex	The size of text shown in correlation plot. Default 8.
number.col	The color of text shown in correlation plot. Default "#C77960".
use.tumorSampleLabel	Logical (Default: FALSE). Rename the 'Tumor_Sample_Barcode' by 'Tumor_Sample_Label'.
...	Other options passed to subMaf

Value

A list contains Fst value of MRS and Hudson estimator of each sample-pair, respectively.

References

Sun R, Hu Z, Sottoriva A, et al. Between-region genetic divergence reflects the mode and tempo of tumor evolution. Nat Genet. 2017;49(7):1015-1024.

Bhatia G, Patterson N, Sankararaman S, Price AL. Estimating and interpreting FST: the impact of rare variants. Genomic Res. 2013;23(9):1514-1521.

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")
calFst(maf)

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