getAltSequence: Check if Ref matches the actual sequence, if so then return...

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

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

Usage

getAltSequence(seqTable, transcriptsTable, transcriptId, pos, ref, alt)

Arguments

seqTable	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.
transcriptId	ensembl transcript id
ref	nucleotides in Ref column
alt	nucleotides in Alt column
trascriptsTable	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.

Value

Altered sequence which combines all its fragments. If Ref doesn't match the actual sequence, raise error

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