findRegions: Find all regions in data above p-value threshold
In ACME: Algorithms for Calculating Microarray Enrichment (ACME)

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1	findRegions(x, thresh = 1e-04)

`x`	An `ACMESetCalc` object
`thresh`	The p-value threshold

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.

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

Sean Davis <sdavis2@mail.nih.gov>

do.aGFF.calc, findClosestGene

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,]

Loading required package: Biobase
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Loading required package: parallel

Attaching package: 'BiocGenerics'

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Working on sample 1
Working on chromosome: 
chr1  chr10  chr11  chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr2  chr20  chr21  chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrX  Working on sample 2
Working on chromosome: 
chr1  chr10  chr11  chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr2  chr20  chr21  chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrX                   Length    TF StartInd EndInd    Sample Chromosome     Start
testsamp1.chr1.1   2720 FALSE        1   2720 testsamp1       chr1  18370933
testsamp1.chr1.2      7  TRUE     2721   2727 testsamp1       chr1 160504242
testsamp1.chr1.3    183 FALSE     2728   2910 testsamp1       chr1 160512520
testsamp1.chr1.4      7  TRUE     2911   2917 testsamp1       chr1 161743296
testsamp1.chr1.5    709 FALSE     2918   3626 testsamp1       chr1 161744293
testsamp1.chr1.6      1  TRUE     3627   3627 testsamp1       chr1 161866419
                       End       Median         Mean
testsamp1.chr1.1 160502834 3.778240e-01 0.4516588005
testsamp1.chr1.2 160511031 1.941371e-04 0.0001449863
testsamp1.chr1.3 161743150 4.560643e-01 0.4888990295
testsamp1.chr1.4 161743722 3.221346e-05 0.0000860163
testsamp1.chr1.5 161866348 3.778240e-01 0.4200206198
testsamp1.chr1.6 161866419 5.729070e-04 0.0005729070