GenomicRegionsFindOverlap: Function to find overlap between GenomicRegions objects

In PREDA: Position Related Data Analysis

Description

Function to find overlap between GenomicRegions objects

Usage

GenomicRegionsFindOverlap(GenomicRegions1, GenomicRegions2 = NULL)

Arguments

GenomicRegions1	Either a GenomicRegions object or a list of GenomicRegions objects
GenomicRegions2	Optiona with default value NULL. Either a GenomicRegions object or a list of GenomicRegions objects.

Details

Input genomic regions object are compared to select overlapping genomic regions that are returned as GenomicRegions objects.

If two single GenomicRegions object are provided, just one comparison is performed and one single GenomicRegions object is returned.

If one single list of GenomicRegions objects is provided as input, then the included GenomicRegions objects are compared to select overlapping GenomicRegions across all of the elements.

If two lists of GenomicRegions objects are provided as input, they must have the same number of elements, because element by element comparison will be performed to identify overlapping GenomicRegions across all of the elements.

Value

Either a single GenomicRegions objec or a list of GenomicRegions objecs.

Author(s)

Francesco Ferrari

See Also

GenomicRegionsComparison, GenomicRegions

Examples

## Not run: 
require(PREDAsampledata)
data(SODEGIRCNanalysisResults)
data(SODEGIRGEanalysisResults)

SODEGIR_GE_UP<-PREDAResults2GenomicRegions(
SODEGIRGEanalysisResults, qval.threshold=0.05,
smoothStatistic.tail="upper", smoothStatistic.threshold=0.5)

SODEGIR_CN_GAIN<-PREDAResults2GenomicRegions(
SODEGIRCNanalysisResults, qval.threshold=0.01,
smoothStatistic.tail="upper", smoothStatistic.threshold=0.1)

SODEGIR_AMPLIFIED<-GenomicRegionsFindOverlap(SODEGIR_GE_UP,
SODEGIR_CN_GAIN)


## End(Not run)

PREDA documentation built on Nov. 8, 2020, 7:40 p.m.