findRegions {ACME} | R Documentation |
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.
findRegions(calcobj, thresh = 1e-04)
calcobj |
An aGFFCalc 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 |
Sean Davis <sdavis2@mail.nih.gov>
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,]