Description Usage Arguments Value
countDNAPatternInAlt
Count the number of DNA pattern in the altered sequence of one transcript. The alter sequence is generated by find the fragment where Pos is in, replace the Ref with Alt in the fragments, and then concatenating all fragments together.
1 2 3 4 5 6 7 | countDNAPatternInAltOneVariant(
variant,
seqTable,
transcriptsTable,
dnaPattern,
transcriptIdCol
)
|
variant |
variant info |
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. |
dnaPattern |
the string pattern that you want to count, for example "ATG" |
transcriptIdCol |
the ensemble transcript id column |
trascriptsTable |
transcripts structure table from ensembl with start and end columns for start and end coordinates of the target regions |
number of DNA pattern
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