ACME (version 2.28.0)

findRegions: Find all regions in data above p-value threshold

Description

After the ACME calculation, each probe is associated with a p-value of enrichment. However, one often wants the contiguous regions associated with runs of p-values above a given p-value threshold.

Usage

findRegions(x, thresh = 1e-04)

Arguments

x

An ACMESetCalc object

thresh

The p-value threshold

Value

A data frame with these columns:

Length

The length of the region in probes

TF

Either TRUE or FALSE; TRUE regions represent regions of enrichment while FALSE regions are the regions between the TRUE regions

StartInd

The starting Index of the region

EndInd

The ending Index of the region

Sample

The sample containing the region

Chromosome

The Chromosome of the region

Start

The starting basepairof the region

End

The ending basepair of the region

Median

The median p-value in the region

Mean

The mean p-value in the region

Details

Runs of p-values above the p-value threshold will be reported as one "region". These can be used for downstream analyses, export to browsers, submitted for transcription factor binding enrichment analyses, etc.

See Also

do.aGFF.calc, findClosestGene

Examples

data(example.agff)
example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
foundregions <- findRegions(example.agffcalc,thresh=0.001)
foundregions[1:6,]