Kc_get: 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_get(
  ID,
  ss,
  ref_genes = "all",
  segfile_folder = "analysis/CONUMEE/Segments",
  log2rfile_folder = "analysis/CONUMEE/log2r",
  arraytype = NULL,
  anno_file = NULL,
  cn_genes = NULL,
  Kc_method = "balanced"
)

Arguments

ID	ID inside Sample sheet and in the Sample_Name.
ss	sample sheet
ref_genes	Granges object with subset of genes to use for cnv analysis.
segfile_folder	Path to folder with segmentation files.
log2rfile_folder	Path to folder with intensities files.
arraytype	Methylation array type
anno_file	anno file CNV.anno object saved as .rds. default CNV_Germline_GSITIC2_BROAD_SNP6.merged.151117.hg19.CNV.txt
cn_genes	Used to subset genes from the reference set. Needed in order to generate new Kc from a reference set, where cn_genes are previously known genes to be altered in a given cn_state. Otherwise use ref_genes.
Kc_method	Choose which Kc you want to use. Either "curated" or "balanced. The first comes from a list of 94 genes manually selected by experts and an uneven proportion of cancers. The second one comes from all genes and balanced proportion of cancer types. default= balanced

Value

GRanges object of the genes of interest "ref_genes" and a cna column with the copy number alterations for each of them.

Author(s)

Izar de Villasante

Examples

data("TrainingSet_Sample_sheet")
ss<-TrainingSet_Sample_sheet[1:56,]
ID="TCGA-19-A6J4-01A-11D-A33U-05"
ss[Sample_Name==ID,]->ss
cna<-Kc_get(ss=ss,ID="TCGA-19-A6J4-01A-11D-A33U-05")
cna

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