utr.annotation (version 1.0.4)

countDNAPatternInAlt: Count the number of DNA pattern in the altered sequence of each transcript.

Description

countDNAPatternInAlt Count the number of DNA pattern in the altered sequence of each transcript, and concatenate the numbers with ";". 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.

Usage

countDNAPatternInAlt(
  variantsTable,
  seqTable,
  transcriptsTable,
  dnaPattern,
  transcriptIdCol
)

Arguments

variantsTable

variants table

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

Value

a list containing values for number of DNA pattern. Can be used to add new column to the variants table.