callpeak-methods: Call enriched bins based on the CSSP model.

In CSSP: ChIP-Seq Statistical Power

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)

## S4 method for signature 'CSSPFit'
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.

Author(s)

Chandler Zuo [e-mail]

Examples

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

CSSP documentation built on Nov. 8, 2020, 8:26 p.m.