Kc_make: Set of functions to obtain Kc from reference copy number...

In ijcBIT/cnv.methyl: cnv.methyl finds copy number alteration from methylation idat files

Set of functions to obtain Kc from reference copy number state.

Description

Set of functions to obtain Kc from reference copy number state.

Usage

Kc_make(
  ss,
  ID,
  arraytype = NULL,
  cncols = c("Amp10", "Amp", "Gains", "HetLoss", "HomDel"),
  segfile_folder = "analysis/CONUMEE/Segments",
  anno_file = NULL,
  ncores = NULL,
  log2rfile_folder = "analysis/CONUMEE/log2r",
  ref_genes = "paper"
)

Arguments

ss	Sample sheet containing purities, cnstate and Sample_Name ids.
ID	ID inside Sample sheet and in the Sample_Name.
arraytype	Methylation array type
cncols	column names containing reference set of genes for each cn state
segfile_folder	Path to folder with segmentation files.
anno_file	anno file CNV.anno object saved as .rds. default CNV_Germline_GSITIC2_BROAD_SNP6.merged.151117.hg19.CNV.txt
ncores	number of cores to use.
log2rfile_folder	Path to folder with intensities files.
ref_genes	Granges object with subset of genes to use for cnv analysis. default = "paper"

Examples

library(cnv.methyl)
data("ss")
Kc_make(ss=ss,cncols=c("Amp","Amp10","Gains"))->a

ijcBIT/cnv.methyl documentation built on Jan. 10, 2023, 7:51 a.m.