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]