Bio.ChIPSeq

Documentation

monoColonalize :: Monad m => Conduit BED m BED

process a sorted BED stream, keep only mono-colonal tags

rpkmBed :: (PrimMonad m, BEDLike b, Vector v Double) => [b] -> Sink BED m (v Double)

calculate RPKM on a set of unique regions. Regions (in bed format) would be kept in memory but not tag file. RPKM: Readcounts per kilobase per million reads. Only counts the starts of tags

rpkmSortedBed :: (PrimMonad m, BEDLike b, Vector v Double) => Sorted (Vector b) -> Sink BED m (v Double)

calculate RPKM on a set of regions. Regions must be sorted. The Sorted data type is used to remind users to sort their data.

countTagsBinBed

Arguments

:: (Integral a, PrimMonad m, Vector v a, BEDLike b)

=> Int

bin size

-> [b]

regions

-> Sink BED m ([v a], Int)

divide each region into consecutive bins, and count tags for each bin and return the number of all tags. Note: a tag is considered to be overlapped with a region only if the starting position of the tag is in the region. For the common sense overlapping, use countTagsBinBed'.

countTagsBinBed'

Arguments

:: (Integral a, PrimMonad m, Vector v a, BEDLike b1, BEDLike b2)

=> Int

bin size

-> [b1]

regions

-> Sink b2 m ([v a], Int)

Same as countTagsBinBed, except that tags are treated as complete intervals instead of single points.

tagCountDistr :: PrimMonad m => Vector v Int => Sink BED m (v Int)

peakCluster

Arguments

:: (BEDLike b, Monad m)

=> [b]

peaks

-> Int

radius

-> Int

cutoff

-> Source m BED

cluster peaks