CSSP (version 1.10.0)

callpeak: Call enriched bins based on the CSSP model.

Description

Call enriched bins based on the CSSP model.

Usage

callpeak(fit, chip, fold = 1.8, min.count = 0, qval = 0.05, method = "", depth = fit@lambday)
"callpeak"(fit, chip, fold = 1.8, min.count = 0, qval = 0.05, method = "", depth = fit@lambday)

Arguments

fit

A CSSPFit-class object containing the fitted CSSP model.

chip

A numeric vector containing the bin counts for the ChIP sample.

fold

A numeric value for the fold change threshold for peak calling.

min.count

A numeric value for the minimum ChIP count threshold for peak calling.

qval

A numeric value for the false-discovery rate to be controlled. Default: 0.05.

method

A character value. By default, "min.count" is used to threshold the ChIP bin counts. If 'method=="post"', "min.count" is used to threshold the posterior bin-level poisson intensities.

depth

A numeric value for the sequencing depth corresponding to the ChIP sample of the "chip" argument. If not provided, sequencing depth of "fit" is used.

Value

A numeric vector of locations for binding bins.

Examples

data( sampleFit )
data( bin.data )
callpeak( sampleFit, chip = bin.data@tagCount, fold = 1, min.count = 0 )