Description Usage Arguments Details Value
getTranscriptIdsForTSSKozakVariants
get the ensembl_transcript_id and kozak_positions for variants in TSS Kozak region (8nt) [AG]..AUGG.
1 | getTranscriptIdsForTSSKozakVariants(variantsTable, transcriptRegions)
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variantsTable |
variants table |
transcriptRegions |
transcripts structure table from ensembl |
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 the transcripts for each variant which its mutation Pos is within TSS Kozak regions) kozak_positions (positions of each nucleotide in Kozak sequence)
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