Generate a grey list from a GreyList object

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Description

Create the actual grey list, based on the threshold calculated by calcThreshold and the read counts from countReads.

Usage

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makeGreyList(obj,maxGap=16384)

Arguments

obj

The GreyList object to create the list for.

maxGap

If the distance between neighbouring grey regions is less than or equal to maxGap, the regions will be merged into one big region.

Details

Create the grey list as a GRanges object. Merge grey regions if they are separated by up to maxGap bp.

Value

The modified GreyList, with the regions added.

Author(s)

Gord Brown

See Also

GreyList, GRanges

Examples

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# load a pre-built GreyList object:
data(greyList)

# calculate the actual regions:
gl <- makeGreyList(gl)