getCodon: Get the codon sequence for transcripts in transcriptIdColumn.
In utr.annotation: Annotate Variants in the Untranslated Regions
Description
Usage
Arguments
Value
Description
getCodon Get the codon sequence for transcripts in transcriptIdColumn.
Usage
1
getCodon(variantsTable, seqTable, transcriptIdColumn, codonRegion)
Arguments
variantsTable
variants table
seqTable
cooresponding sequence table from Ensembl DB (either 5' UTR sequence or 3' UTR sequence). Have two columns: ensembl_transcript_id and seq
transcriptIdColumn
the name of the transcript id column for the codon region
codonRegion
"startCodon" or "stopCodon"
Value
A list containing codon sequences (NA if the transcript id in that row is NA). If transcriptIdColumn does not exist in the variantsTable, return NA
utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.
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Description Usage Arguments Value
Description
getCodon Get the codon sequence for transcripts in transcriptIdColumn.
Usage
1 | getCodon(variantsTable, seqTable, transcriptIdColumn, codonRegion)
|
Arguments
variantsTable |
variants table |
seqTable |
cooresponding sequence table from Ensembl DB (either 5' UTR sequence or 3' UTR sequence). Have two columns: ensembl_transcript_id and seq |
transcriptIdColumn |
the name of the transcript id column for the codon region |
codonRegion |
"startCodon" or "stopCodon" |
Value
A list containing codon sequences (NA if the transcript id in that row is NA). If transcriptIdColumn does not exist in the variantsTable, return NA
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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