This function relates found 'cher's (ChIP-enriched regions) to annotated genomic features, such as transcripts.
Object of class
up to how many bases upstream of annotated genomic features should chers be counted as related to that feature (see details)
logical; extended output to STDOUT?
chers will be counted as related to genomic features, if
their middle position is located between start and end position of the feature
their middle position is located not more than argument
upstream bases upstream of the feature start
One can visualize such cher-feature relations as a graph using
the Bioconductor package
See the script 'graphChers2Transcripts.R' in Ringo's scripts
directory for an example.
An object of class
cherList with for each cher the elements
typeInside filled in with the names
of the features that have been related to.
# see findChersOnSmoothed for an example
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