Nothing
## ----style, echo=FALSE, results="asis", message=FALSE-------------------------
BiocStyle::markdown()
knitr::opts_chunk$set(tidy = FALSE,
warning = FALSE,
message = FALSE)
## -----------------------------------------------------------------------------
library(sangeranalyseR)
## -----------------------------------------------------------------------------
inputFilesPath <- system.file("extdata/", package = "sangeranalyseR")
A_chloroticaFdReadFN <- file.path(inputFilesPath,
"Allolobophora_chlorotica",
"RBNII",
"Achl_RBNII396-13_1_F.ab1")
## -----------------------------------------------------------------------------
singleRead <- SangerRead(readFeature = "Forward Read",
readFileName = A_chloroticaFdReadFN)
## -----------------------------------------------------------------------------
qualityBasePlot(singleRead)
## ----results="hide"-----------------------------------------------------------
updateQualityParam(singleRead,
TrimmingMethod = "M1",
M1TrimmingCutoff = 0.0003,
M2CutoffQualityScore = NULL,
M2SlidingWindowSize = NULL)
## -----------------------------------------------------------------------------
writeFastaSR(singleRead)
## ----eval=FALSE---------------------------------------------------------------
# generateReportSR(singleRead)
## -----------------------------------------------------------------------------
rawDataDir <- system.file("extdata", package = "sangeranalyseR")
inputFilesParentDir <- file.path(rawDataDir, "Allolobophora_chlorotica", "ACHLO")
contigName <- "Achl_ACHLO006-09"
suffixForwardRegExp <- "_[0-9]*_[F].ab1"
suffixReverseRegExp <- "_[0-9]*_[R].ab1"
## -----------------------------------------------------------------------------
sangerContig <- SangerContig(parentDirectory = inputFilesParentDir,
contigName = contigName,
suffixForwardRegExp = suffixForwardRegExp,
suffixReverseRegExp = suffixReverseRegExp)
## ----eval=FALSE---------------------------------------------------------------
# launchAppSC(sangerContig)
## -----------------------------------------------------------------------------
writeFastaSC(sangerContig)
## ----eval=FALSE---------------------------------------------------------------
# generateReportSC(sangerContig)
## -----------------------------------------------------------------------------
rawDir <- system.file("extdata", package="sangeranalyseR")
parentDir <- file.path(rawDir, "Allolobophora_chlorotica", "RBNII")
suffixForwardRegExp <- "_[F]_[0-9]*.ab1"
suffixReverseRegExp <- "_[R]_[0-9]*.ab1"
## ----eval=FALSE---------------------------------------------------------------
# sangerAlignment <-
# SangerAlignment(parentDirectory = parentDir,
# suffixForwardRegExp = suffixForwardRegExp,
# suffixReverseRegExp = suffixReverseRegExp,)
## ----eval=FALSE---------------------------------------------------------------
# launchAppSA(sangerAlignment)
## ----eval=FALSE---------------------------------------------------------------
# writeFastaSA(sangerAlignment)
## ----eval=FALSE---------------------------------------------------------------
# generateReportSA(sangerAlignment)
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