estimateDistFun: Estimate the Distance Function

In Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Description

Estimates the function that models how the expected number of counts decreases with increasing distance.

Usage

estimateDistFun(cd, method = "cubic", plot = TRUE, outfile = NULL)

Arguments

cd	A chicagoData object.
method	Choice of method: "cubic" is currently the only allowed option, which fits a cubic function with linear extrapolation, on a log-log scale.

plot	Output a diagnostic plot.
outfile	If NULL, plot to current device. Otherwise, plot to the .pdf file outfile.

Details

By default, we look in 75 distance bins, and a cubic fit is used. For distances that lie outside of the bin boundaries, it is assumed that the function is log-linear, with continuity of f and its first derivative on the log-scale.

Value

An object of class chicagoData, with the parameters of the distance function present as params(cd)$distFunParams.

Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

See Also

chicagoPipeline, plotDistFun

Examples

data(cdUnitTest)
estimateDistFun(cdUnitTest)

Chicago documentation built on Nov. 8, 2020, 8:15 p.m.