ranges2annot: ranges2annot
In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries
Description
Usage
Arguments
Value
See Also
Examples
Description
hierarchical annotation of a Genomic Range as promoter, exon or intron.
Usage
1
ranges2annot(ranges, annot, showClasses = NULL)
Arguments
ranges
The Genomics Ranges object, for example extracted from a
RangedSummarizedExperiment object with the rowRanges
command.
annot
A Genomics Ranges object providing enough information for
inferring promoters, exons and introns. Typically GENCODE.
Value
A factor of same length as the GRanges object, indicating if the
interval is promoter, exon, intron or unknown.
See Also
Other smallCAGEqc annotation functions: hannot,
hierarchAnnot, mapStats,
plotAnnot, ranges2genes
Examples
1
2
3
4
## Not run:
rowRanges(l1)$annotation <- ranges2annot(rowRanges(l1), gff)
## End(Not run)
charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.
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Description Usage Arguments Value See Also Examples
Description
hierarchical annotation of a Genomic Range as promoter, exon or intron.
Usage
1 | ranges2annot(ranges, annot, showClasses = NULL)
|
Arguments
ranges |
The Genomics Ranges object, for example extracted from a
RangedSummarizedExperiment object with the |
annot |
A Genomics Ranges object providing enough information for inferring promoters, exons and introns. Typically GENCODE. |
Value
A factor of same length as the GRanges object, indicating if the interval is promoter, exon, intron or unknown.
See Also
Other smallCAGEqc annotation functions: hannot,
hierarchAnnot, mapStats,
plotAnnot, ranges2genes
Examples
1 2 3 4 | ## Not run:
rowRanges(l1)$annotation <- ranges2annot(rowRanges(l1), gff)
## End(Not run)
|
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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