hiReadsProcessor (version 1.8.2)

doRCtest: Test if pattern aligns better in +/- orientation.

Description

Given a fixed length pattern sequence and variable length subject sequences, the function roughly finds which orientation of pattern yields the most hits. The function doing the heavylifting is vcountPattern. This is an accessory function used in function listed under See Also section below.

Usage

doRCtest(subjectSeqs = NULL, patternSeq = NULL, qualityThreshold = 0.5,
  parallel = TRUE)

Arguments

subjectSeqs

DNAStringSet object containing sequences to be searched for the pattern.

patternSeq

DNAString object or a sequence containing the query sequence to search.

qualityThreshold

percent of patternSeq to match. Default is 0.50, half match. This is supplied to max.mismatch parameter of vcountPattern as round(nchar(patternSeq)*(1-qualityThreshold)).

parallel

use parallel backend to perform calculation with BiocParallel. Defaults to FALSE. If no parallel backend is registered, then a serial version is ran using SerialParam.

Value

• patternSeq that aligned the best.

See Also

pairwiseAlignSeqs, vpairwiseAlignSeqs, primerIDAlignSeqs

Examples

subjectSeqs <- c("CCTGAATCCTGGCAATGTCATCATC", "ATCCTGGCAATGTCATCATCAATGG",
"ATCAGTTGTCAACGGCTAATACGCG", "ATCAATGGCGATTGCCGCGTCTGCA",
"CCGCGTCTGCAATGTGAGGGCCTAA", "GAAGGATGCCAGTTGAAGTTCACAC")
subjectSeqs <- xscat("AAAAAAAAAA", subjectSeqs)
doRCtest(subjectSeqs, "TTTTTTTTT")