getTranscriptIdsForTSSKozakVariants: Find the ensembl_transcript_id and kozak_positions for...
In utr.annotation: Annotate Variants in the Untranslated Regions

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)

`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)

utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.