setAllelePhase {sangerseqR} | R Documentation |
Parses the Primary and Secondary Sequences into Reference and Alternate Alleles
setAllelePhase(obj, refseq, trim5 = 0, trim3 = 0) ## S4 method for signature 'sangerseq' setAllelePhase(obj, refseq, trim5 = 0, trim3 = 0)
obj |
|
refseq |
DNAString for character string of reference allele sequence. |
trim5 |
Number of bases to trim from the beginning of the sequence. |
trim3 |
Number of bases to trim from the end of the sequence. |
When multiple heterozygous basecalls are made, it is generally unclear which calls are in phase with each other. This function takes a reference sequence for one of the alleles to match the primary and secondary basecalls as reference or alternate allele.
A sangerseq
object with the Reference Allele in the
primarySeq slot and the Alternate Allele in the secondarySeq slot.
makeBaseCalls
, chromatogram
,
sangerseq
#Load Sequences hetsangerseq <- readsangerseq(system.file("extdata", "heterozygous.ab1", package = "sangerseqR")) homosangerseq <- readsangerseq(system.file("extdata", "homozygous.scf", package = "sangerseqR")) #Make calls on heterozygous sequence to be parsed hetcalls <- makeBaseCalls(hetsangerseq, ratio = 0.33) #Need a reference sequence to set phase. Can get from annotation #(e.g. Refseq) or another sanger sequencing file ref <- subseq(primarySeq(homosangerseq, string = TRUE), start = 30, width = 500) #Set the phase hetseqalleles <- setAllelePhase(hetcalls, ref, trim5 = 50, trim3 = 100) #Align to compare alleles pa <- pairwiseAlignment(primarySeq(hetseqalleles), secondarySeq(hetseqalleles), type = "global-local") writePairwiseAlignments(pa)