PREDA (version 1.18.0)

PREDAResults2GenomicRegions: identify significant genomic regions from a PREDAResults object

Description

identify significant genomic regions from a PREDAResults object

Usage

# PREDAResults2GenomicRegions(.Object, qval.threshold=0.05,
# use.referencePositions=TRUE, smoothStatistic.tail=NULL,
# smoothStatistic.threshold=NULL)
PREDAResults2GenomicRegions(.Object, ...)

Arguments

.Object

Object of class PREDAResults or PREDADataAndResults

...

See below

qval.threshold:

q-value threshold used to identify significant genomic regions

use.referencePositions:

Logical, if TRUE the input reference positions used for PREDA analysis wil be used to identify significant genomic regions boundaries as well.

smoothStatistic.tail:

Possible values are "upper" or "lower". This parameter specify if only one tail of the smoothed statististic distribution must be considered. If it is NULL, both tails are used and smoothStatistic.threshold is ignored.

smoothStatistic.threshold:

Threshold on smoothStatistic values to select significant genomic regions.

Value

A list of genomic regions objects

Details

A list og genomic regions objects is returned: one GenomicRegions object for each analysis in the input PREDAresults.

A NULL element is included in the output list whenever no siginifcant regions are identified.

Examples

## Not run: 
# require(PREDAsampledata)
# 
# data(GEanalysisResults)
# 
# genomic_regions_UP<-PREDAResults2GenomicRegions(GEanalysisResults
# , qval.threshold=0.05, smoothStatistic.tail="upper",
# smoothStatistic.threshold=0.5)
# 
# ## End(Not run)