setAllelePhase: Set Reference and Alternate Alleles

In jonathonthill/sangerseqR: Tools for Sanger Sequencing Data in R

Set Reference and Alternate Alleles

Description

Parses the Primary and Secondary Sequences into Reference and Alternate Alleles

Usage

setAllelePhase(obj, refseq, trim5 = 0, trim3 = 0)

## S4 method for signature 'sangerseq'
setAllelePhase(obj, refseq, trim5 = 0, trim3 = 0)

Arguments

obj	sangerseq class object
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.

Details

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.

Value

A sangerseq object with the Reference Allele in the primarySeq slot and the Alternate Allele in the secondarySeq slot.

See Also

makeBaseCalls, chromatogram, sangerseq

Examples

#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)

jonathonthill/sangerseqR documentation built on July 1, 2023, 4:55 p.m.