calFst: calFst

Description Usage Arguments Value References Examples

View source: R/calFst.R

Description

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

Usage

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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

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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.