fitNullModel: Fit Null distribution of copy number variation signals

In hshdndx/new-to-CNV: patternCNV: a versatile tool for detecting copy number changes from exome-seq data

Description

This function fits null distribution of copy number variation signals, according to given reference/normal samples. The underlying assumption is reference/normal samples have very few number of CNV events, comparing to case/disease samples.

Usage

fitNullModel(refdata.name, type = "autosome", is.plot = FALSE, capture.only = TRUE)

Arguments

refdata.name	an object of PatCNVData-class of reference/normal samples
type	a character of either "autosome" or "all" to indicate if CNV signals of chr1-22 or all of the chromosomes are used for fitting Null distribution
is.plot	a logical value indicating if the null distribution is plotted
capture.only	a logical value indicating if only captured exons should be considered

Value

This function returns a list of null distribution model that is used by estimateFDR

Author(s)

Chen Wang

See Also

estimateFDR

Examples

#=== load simulated data with pre-computed coverage and CNV
data(sim.cnvData)

#=== fit null distribution of CNV signals and plot distribution of CNV signals (log2ratio)
null.model <- fitNullModel(sim.cnvData,"all",TRUE)

hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.