findPeaks-methods: findPeaks

In sheng-liu/SeqData: A data structure and four simple tools build upon it for sequencing data analysis

Description

Find reads enriched regions using poission distribution model.

Usage

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

• peakTable.csv A csv file contaning information about the significantly enriched regions, including chromosome,start,end,peakPositions,peakCoverageSums,rpkm.peakCoverageSums,chipPeakHeights,controlPeakHeights,p.values,fdr,foldChange.

• coverageView slot A RleViews object containing Views of the peak regions.

Usage

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

Examples

#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.