Description Usage Arguments Details Value
Find the ensembl_transcript_id and codon postions for one variant
1 2 3 4 5 6 7 | getTranscriptIdsForOneCodonVariant(
variant,
transcriptRegions,
checkRegion,
start,
end
)
|
variant |
one row of variants table |
transcriptRegions |
transcripts structure table from ensembl |
checkRegion |
check if a transcript within a region stopCodon or startCodon |
start |
column name of the start region of checkRegion in transcripts structure table |
end |
column name of the end region of checkRegion in transcripts structure table |
For each variant, get all transcripts and extract their checkRegion's coordinates. For each transcript, check if the mutation Pos is within the region, if so, add that transcript's ensembl_transcript_id. If the mutation Pos is within multiple transcripts checkRegions, the transcripts ids are concatenate into one string with ";".
A data table containing two columns: ensembl_transcript_id (id of transcripts for each variant which its mutation Pos is within those transcripts checkRegion.) codon_positions (positions of each nucleotides in the codon)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.