Bio.GO.GREAT

Documentation

data AssocRule

How to associate genomic regions with genes

Constructors

BasalPlusExtension Int Int Int

Upstream, downstream and extension

TwoNearest

Not implemented

OneNearest

Not implemented

defaultAssocRule :: AssocRule

The default rule is defined as -5k ~ +1k around TSSs, plus up to 1000k extension.

getRegulatoryDomains :: AssocRule -> [Gene a] -> [(BED3, a)]

Given a gene list and the rule, compute the rulatory domain for each gene

read3DContact :: FilePath -> Source (ResourceT IO) (BED3, BED3)

Read 3D contacts from a file, where each line contains 6 fields separated by Tabs corresponding to 2 interacting loci. Example: chr1 [TAB] 11 [TAB] 100 [TAB] chr2 [TAB] 23 [TAB] 200

get3DRegulatoryDomains

Arguments

:: (Monad m, Ord a)

=> [Gene a]

Genes

-> Int

Upstream

-> Int

Downstream

-> Conduit (BED3, BED3) m (BED3, a)

3D regulatory domains of a gene include the gene's promoter and regions that contact with the gene's promoter.