calNeiDist: calNeiDist

Description Usage Arguments Value References Examples

View source: R/calNeiDist.R

Description

Nei's distance of CCF for sample/tumor pair.

Usage

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calNeiDist(
  maf,
  patient.id = NULL,
  withinTumor = FALSE,
  min.ccf = 0,
  plot = TRUE,
  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.

withinTumor

Calculate between-region heterogeneity within tumor. (Default: FALSE).

min.ccf

Specify the minimum CCF. Default 0.

plot

Logical (Default: TRUE).

use.circle

Logical (Default: TRUE). Whether to use "circle" 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

Nei's genetic distance matrix and heatmap of sample-pairs from the same patient

References

Lee JK, Wang J, Sa JK, et al. Spatiotemporal genomic architecture informs precision oncology in glioblastoma. Nat Genet. 2017;49(4):594-599.

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")
calNeiDist(maf)

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