findPeaks-methods: findPeaks

Description Usage Arguments Details Value Usage Examples

Description

Find reads enriched regions using poission distribution model.

Usage

1
findPeaks(bamFile.chip) # this roxygen directive does not working

Arguments

obj.chip

SeqData object containing information on chip.

obj.control

SeqData object containing information on control.

bamFile.control

Full path to control bam file.

description

Optional. User can input short desciption for the output file, it will show up in the file name of the output file.

bamFie.chip

Full path to chip bam file.

Details

possibility of a reads been random possibility of peak heights (base coverage) at specific location is esitmated from the average (lambda) coverage of the peak region, 1kb region, 5kb region and 10 kb regions. This is to account for local fluctuations.

Value

Usage

findPeaks(obj.chip=NULL,obj.control=NULL,bamFile.chip=character(0),bamFile.control=character(0),fdr.max=1e-5,foldChange.min=2)

Examples

1
2
3
4
5
6
7
#findPeaks(bamFile.chip)
#findPeaks(bamFile.chip,bamFile.control)
#findPeaks(obj.chip)
#findPeaks(obj.chip,obj.control)
#findPeaks(obj.chip,obj.control,bamFile.chip,bamFile.control)
# to view coverageView slot
# coverageView(obj.chip)[[1]]

sheng-liu/SeqData documentation built on May 29, 2019, 9:22 p.m.