CDSSet: Container for coding sequence (CDS) annotation information
In IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Description
Usage
Arguments
Details
Value
Author(s)
References
Description
A container for coding sequence annotation information.
Usage
1
CDSSet(cds)
Arguments
cds
A data.frame object containing CDS annotation. See details for required columns.
Details
This object can be generated automatically from getCDS, or can be be generated manually by creating a new CDSSet from a data.frame with the following columns:
chrom, the chromosome name (NB: chromosome names must match when running analyzeORF).
strand, the strand,
cdsStart, the genomic start of the coding sequence (beware of 0/1-frame issues), and
cdsEnd, the genomic end of the coding sequence (beware of 0/1-frame issues).
The CDSset object is used with analyzeORF if annotated TSS should be analyzed.
For an example, see getCDS.
Value
A CDSSet object.
Author(s)
Kristoffer Vitting-Seerup, Johannes Waage
References
Vitting-Seerup K, et al: spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 2014, 15:81.
IsoformSwitchAnalyzeR documentation built on Nov. 8, 2020, 5:36 p.m.
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Description Usage Arguments Details Value Author(s) References
Description
A container for coding sequence annotation information.
Usage
1 | CDSSet(cds)
|
Arguments
cds |
A |
Details
This object can be generated automatically from getCDS, or can be be generated manually by creating a new CDSSet from a data.frame with the following columns:
chrom, the chromosome name (NB: chromosome names must match when running analyzeORF).
strand, the strand,
cdsStart, the genomic start of the coding sequence (beware of 0/1-frame issues), and
cdsEnd, the genomic end of the coding sequence (beware of 0/1-frame issues).
The CDSset object is used with analyzeORF if annotated TSS should be analyzed.
For an example, see getCDS.
Value
A CDSSet object.
Author(s)
Kristoffer Vitting-Seerup, Johannes Waage
References
Vitting-Seerup K, et al: spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 2014, 15:81.
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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