scna: - Deprecated! USe Kc_make – Function to obtain mean...

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

— Deprecated! USe Kc_make —- Function to obtain mean intercept and variance from a reference gene set and a particular copy number state

Description

— Deprecated! USe Kc_make —- Function to obtain mean intercept and variance from a reference gene set and a particular copy number state

Usage

scna(ID, log2file, segfile, ss, cn, ref_genes = "all")

Arguments

ID	name of sample. Must be in Sample_Name column.
log2file	file with log2r values, which are the fitted log intensity value against the reference set returned by CNV.fit function from CONUMEE.
segfile	file containing segment data from conumee. The segments are generated with CONUMEE CNV.segment(CNV.detail(CNV.bin(fit)))
ss	Sample sheet containing purities, cnstate and Sample_Name ids.
cn	Sample sheet column name containing reference gene set for that cn.
ref_genes	Granges object with subset of genes to use for cnv analysis. default = "paper"

Value

dataframe with input data for linear model. Int, mean and Var .

Examples

ss<-data.table::fread("analysis/ChAMP/Sample_Sheet.txt")
res<-scna(ID="TCGA-05-4405-01A-21D-1856-05",ss=ss,ref_genes="paper",cn="Amp",
log2file="analysis/CONUMEE/log2/TCGA-05-4405-01A-21D-1856-05_log2.txt",
segfile="analysis/CONUMEE/Segments_TCGA-05-4405-01A-21D-1856-05.txt")
res

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