findRegions {ACME}R Documentation

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(calcobj, thresh = 1e-04)

Arguments

calcobj An aGFFCalc object
thresh The p-value threshold

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.

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

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

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,]

[Package ACME version 1.2.1 Index]