refseq_CDScoords: Extract the coding sequences (CDS) coordinates from a...
In refseqR: Common Computational Operations Working with RefSeq Entries (GenBank)
View source: R/refseq_CDScoords.R
refseq_CDScoords R Documentation
Extract the coding sequences (CDS) coordinates from a transcript accession
Description
refseq_CDScoords() Parses a transcript accession (RefSeq format) and extract the CDS coordinates.
The CDS coordinates refer to the mRNA molecule.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_CDScoords(transcript)
Arguments
transcript
A character string of the single/multiple transcript id.
Value
An IRanges object with the start and end position of the CDS of the
putative mRNAs.
Author(s)
Jose V. Die
See Also
refseq_CDSseq
Examples
transcript = c("XM_004487701")
refseq_CDScoords(transcript)
transcript = c("XM_004487701", "XM_004488493")
refseq_CDScoords(transcript)
refseqR documentation built on Oct. 30, 2024, 1:06 a.m.
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View source: R/refseq_CDScoords.R
| refseq_CDScoords | R Documentation |
Extract the coding sequences (CDS) coordinates from a transcript accession
Description
refseq_CDScoords() Parses a transcript accession (RefSeq format) and extract the CDS coordinates.
The CDS coordinates refer to the mRNA molecule.
Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.
Usage
refseq_CDScoords(transcript)
Arguments
transcript |
A character string of the single/multiple transcript id. |
Value
An IRanges object with the start and end position of the CDS of the
putative mRNAs.
Author(s)
Jose V. Die
See Also
refseq_CDSseq
Examples
transcript = c("XM_004487701")
refseq_CDScoords(transcript)
transcript = c("XM_004487701", "XM_004488493")
refseq_CDScoords(transcript)
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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