CNregions.mod: CNregions.mod Modified CNregions function from the facets...

In AxelitoMartin/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

CNregions.mod Modified CNregions function from the facets package to handle small sample sizes.

Description

CNregions.mod Modified CNregions function from the facets package to handle small sample sizes.

Usage

CNregions.mod(
  seg,
  epsilon = 0.005,
  adaptive = FALSE,
  rmCNV = FALSE,
  cnv = NULL,
  frac.overlap = 0.5,
  rmSmallseg = TRUE,
  nProbes = 15
)

Arguments

seg	a segmentation file containing the segmentation information of multiple samples
epsilon	the maximum Euclidean distance between adjacent probes tolerated for denying a nonredundant region. epsilon=0 is equivalent to taking the union of all unique break points across the n samples.
adaptive	Vector of length-m lasso penalty terms.
rmCNV	If TRUE, remove germline CNV.
cnv	A data frame containing germline CNV data.
frac.overlap	A parameter needed to be explain.
rmSmallseg	If TRUE, remove small segment.
nProbes	The segment length threshold below which the segment will be removed if rmSmallseq = TRUE.

Value

reducedM : A matrix ready for plotting.

Examples

library(gnomeR)
library(dplyr)
samples <-
as.character(unique(mut$Tumor_Sample_Barcode))[
sample(1:length(unique(mut$Tumor_Sample_Barcode)), 100, replace=FALSE)]
CNregions.mod(seg %>% filter(ID %in% samples))[1:5,1:5]

AxelitoMartin/gnomeR documentation built on April 21, 2022, 3:01 p.m.