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## ----style, eval=TRUE, echo=FALSE, results="asis"--------------------------
BiocStyle::latex()
## ----knitr, eval=TRUE, include=FALSE---------------------------------------
library(knitr, quietly=TRUE)
library(sangerseqR, quietly=TRUE)
library(Biostrings, quietly=TRUE)
opts_chunk$set(tidy=TRUE)
#modified from:
#https://github.com/yihui/knitr-examples/blob/master/077-wrap-output.md
hook_output = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
n <- 90
x <- knitr:::split_lines(x)
# any lines wider than n should be wrapped
if (any(nchar(x) > n)) {
x <- gsub(sprintf('(.{%d})', n), "\\1\n## ", x)
}
hook_output(x, options)
})
## --------------------------------------------------------------------------
hetab1 <- read.abif(system.file("extdata",
"heterozygous.ab1",
package="sangerseqR"))
str(hetab1, list.len=20)
## --------------------------------------------------------------------------
homoscf <- read.scf(system.file("extdata",
"homozygous.scf",
package="sangerseqR"))
str(homoscf)
## --------------------------------------------------------------------------
#from a sequence file object
homosangerseq <- sangerseq(homoscf)
#directly from the file
hetsangerseq <- readsangerseq(system.file("extdata",
"heterozygous.ab1",
package="sangerseqR"))
str(hetsangerseq)
## --------------------------------------------------------------------------
#default is to return a DNAString object
Seq1 <- primarySeq(homosangerseq)
reverseComplement(Seq1)
#can return as string
primarySeq(homosangerseq, string=TRUE)
## --------------------------------------------------------------------------
chromatogram(hetsangerseq, width=200, height=2, trim5=50, trim3=100,
showcalls='both', filename="chromatogram.pdf")
## --------------------------------------------------------------------------
hetcalls <- makeBaseCalls(hetsangerseq, ratio=0.33)
hetcalls
## --------------------------------------------------------------------------
chromatogram(hetcalls, width=100, height=2, trim5=50, trim3=100,
showcalls='both', filename="chromatogram2.pdf")
## --------------------------------------------------------------------------
ref <- subseq(primarySeq(homosangerseq, string=TRUE), start=30, width=500)
hetseqalleles <- setAllelePhase(hetcalls, ref, trim5=50, trim3=300)
hetseqalleles
## --------------------------------------------------------------------------
pa <- pairwiseAlignment(primarySeq(hetseqalleles)[1:400],
secondarySeq(hetseqalleles)[1:400],
type="global-local")
writePairwiseAlignments(pa)
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