getCpgFeatures: Generate feature sets based on CpG island, shore, and shelf...
In jeffbhasin/goldmine: goldmine: Genomic context annotation for any set of genomic ranges using UCSC Genome Browser tables
Description
Uses the "cpgIslandExt" table to generate shore (+/- 2kb from islands) and shelf (+/- 2kb from shores) regions. Will only function for genomes with this table available. Can be concatenated using c() with other tables, such as from getFeatures(), and provided as input for the "features" argument of goldmine().
Usage
1
getCpgFeatures(genome, cachedir)
Arguments
genome
The UCSC name specific to the genome of the query coordinates (e.g. "hg19", "hg18", "mm10", etc)
cachedir
A path to a directory where a local cache of UCSC tables are stored. If equal to NULL (default), the data will be downloaded to temporary files and loaded on the fly. Caching is highly recommended to save time and bandwidth.
jeffbhasin/goldmine documentation built on Nov. 13, 2019, 9:11 a.m.
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Description
Uses the "cpgIslandExt" table to generate shore (+/- 2kb from islands) and shelf (+/- 2kb from shores) regions. Will only function for genomes with this table available. Can be concatenated using c() with other tables, such as from getFeatures(), and provided as input for the "features" argument of goldmine().
Usage
1 | getCpgFeatures(genome, cachedir)
|
Arguments
genome |
The UCSC name specific to the genome of the query coordinates (e.g. "hg19", "hg18", "mm10", etc) |
cachedir |
A path to a directory where a local cache of UCSC tables are stored. If equal to |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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