ranges2genes: ranges2genes
In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
ranges2genes R Documentation
ranges2genes
Description
Assign gene symbol(s) to Genomic Ranges.
Usage
ranges2genes(ranges, genes)
Arguments
ranges
GenomicRanges::GRanges object, for example extracted from
a SummarizedExperiment::RangedSummarizedExperiment object with the
SummarizedExperiment::rowRanges command.
genes
A GRanges object containing gene_name metadata.
Details
This private (non-exported) function is used to assign gene symbols
to genomic ranges. It is run by annotateCTSS, which has to
be run before CTSStoGenes.
Value
A S4Vectors::Rle factor of same length as the GRanges object,
indicating one gene symbol or a semicolon-separated list of gene symbols for each
range. The levels are alphabetically sorted.
Author(s)
Charles Plessy
See Also
CTSScoordinatesGR, exampleZv9_annot
Other CAGEr annotation functions:
annotateCTSS(),
plotAnnot(),
ranges2annot(),
ranges2names()
Other CAGEr gene expression analysis functions:
CTSStoGenes(),
GeneExpDESeq2()
Examples
CAGEr:::ranges2genes(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)
charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.
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| ranges2genes | R Documentation |
ranges2genes
Description
Assign gene symbol(s) to Genomic Ranges.
Usage
ranges2genes(ranges, genes)
Arguments
ranges |
|
genes |
A GRanges object containing |
Details
This private (non-exported) function is used to assign gene symbols
to genomic ranges. It is run by annotateCTSS, which has to
be run before CTSStoGenes.
Value
A S4Vectors::Rle factor of same length as the GRanges object,
indicating one gene symbol or a semicolon-separated list of gene symbols for each
range. The levels are alphabetically sorted.
Author(s)
Charles Plessy
See Also
CTSScoordinatesGR, exampleZv9_annot
Other CAGEr annotation functions:
annotateCTSS(),
plotAnnot(),
ranges2annot(),
ranges2names()
Other CAGEr gene expression analysis functions:
CTSStoGenes(),
GeneExpDESeq2()
Examples
CAGEr:::ranges2genes(CTSScoordinatesGR(exampleCAGEexp), exampleZv9_annot)
R Package Documentation
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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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