getAltSequence

sequences table containing columns: ensembl_transcript_id and seq. seq is the sequence of a seqType region: e.g. 5' UTR sequence or 3' UTR sequence. The seqTable is output from function getSeqTable.

seqTable

transcriptId

transcripts structure table, must have 4 columns: ensembl_transcript_id, start, end, strand.
start: start coordinate column in transcriptsTable for target region, for example "utr5_start", "utr3_start", or "genomic_coding_start"
end: end coordinate columns in transcriptsTable for target region, for example "utr5_end", "utr3_end", or "genomic_coding_end"
strand is the strand of the transcript.

trascriptsTable

Check if Ref matches the actual sequence, if so then return altered sequence after replacing Ref with Alt. The sequence can have multiple fragments, only check the fragment which pos &gt;= fragment_start &amp; pos &lt;= fragment_end

internal

A fast, user-friendly tool for annotating potential deleterious variants in the untranslated regions for both human and mouse species. Y Liu, JD Dougherty (2021) <doi:10.1101/2021.06.23.449510>.

Yating Liu

utr.annotation

Annotate Variants in the Untranslated Regions

Joseph D. Dougherty

getAltSequence function

Check if Ref matches the actual sequence, if so then return altered sequence after replacing Ref with Alt. The sequence can have multiple fragments, only check the fragment which pos &gt;= fragment_start &amp; pos &lt;= fragment_end — getAltSequence

Check if Ref matches the actual sequence, if so then return altered sequence after replacing Ref with Alt. The sequence can have multiple fragments, only check the fragment which pos &gt;= fragment_start &amp; pos &lt;= fragment_end

getAltSequence: Check if Ref matches the actual sequence, if so then return altered sequence after replacing Ref with Alt. The sequence can have multiple fragments, only check the fragment which pos >= fragment_start & pos <= fragment_end

Description

Usage

Arguments

Value