DR2S_: R6 Class '"DR2S"'

In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description

An object representing a DR2S analysis.

Public fields

mapInit

<MapList>; the initial mapping of long reads to reference.

lrpartition

<PartList>; the partitioning of full-length mapped long reads into different haplotypes.

mapIter

<MapList>; the mapping of A and B reads to consensus sequences produced in the previous step.

srpartition

<PartList>; the partitioning of mapped short reads into different haplotypes.

mapFinal

<MapList>; the mapping of A, B, and short reads to consensus sequences produced in the previous step.

remap

<MapList>; the mapping of A, B, and short reads to consensus sequences produced in the previous step.

consensus

<ConsList>; final consensus sequences for A and B.

Methods

Public methods

• DR2S_$new()

• DR2S_$cache()

• DR2S_$clear()

• DR2S_$cleanup()

• DR2S_$print()

• DR2S_$run_()

• DR2S_$getConfig()

• DR2S_$setConfig()

• DR2S_$getDatadir()

• DR2S_$getOutdir()

• DR2S_$getMicrosatellite()

• DR2S_$getForceMapping()

• DR2S_$getThreshold()

• DR2S_$getDistAlleles()

• DR2S_$getIterations()

• DR2S_$getLrdMapper()

• DR2S_$getLrdType()

• DR2S_$getLrdDir()

• DR2S_$getLongreads()

• DR2S_$getSrdMapper()

• DR2S_$getSrdType()

• DR2S_$getSrdDir()

• DR2S_$getShortreads()

• DR2S_$getPipeline()

• DR2S_$getOpts()

• DR2S_$getSampleId()

• DR2S_$getLocus()

• DR2S_$getReference()

• DR2S_$getPlatform()

• DR2S_$getFormat()

• DR2S_$setFormat()

• DR2S_$getDetails()

• DR2S_$setDetails()

• DR2S_$getSampleDetails()

• DR2S_$getStats()

• DR2S_$setStats()

• DR2S_$getLimits()

• DR2S_$setLimits()

• DR2S_$getHapTypes()

• DR2S_$setHapTypes()

• DR2S_$getRefPath()

• DR2S_$setRefPath()

• DR2S_$getHomozygous()

• DR2S_$setHomozygous()

• DR2S_$getRefSeq()

• DR2S_$getPileup()

• DR2S_$getSnpMatrix()

• DR2S_$getPartition()

• DR2S_$getHapList()

• DR2S_$getLatestRefPath()

• DR2S_$getLatestRef()

• DR2S_$getMapTag()

• DR2S_$getGroupPileup()

• DR2S_$getLrdMapFun()

• DR2S_$getSrdMapFun()

• DR2S_$absPath()

• DR2S_$relPath()

• DR2S_$hasMapInit()

• DR2S_$hasLrdPartition()

• DR2S_$hasHapList()

• DR2S_$hasMapIter()

• DR2S_$hasMapFinal()

• DR2S_$checkGetShortreads()

• DR2S_$hasShortreads()

• DR2S_$checkGetLongreads()

• DR2S_$hasLongreads()

• DR2S_$plotCoverage()

• DR2S_$plotGroupCoverage()

• DR2S_$plotBasecallFrequency()

• DR2S_$plotGroupBasecallFrequency()

• DR2S_$plotPartitionHistogram()

• DR2S_$plotPartitionTree()

• DR2S_$plotPartitionRadar()

• DR2S_$polymorphicPositions()

• DR2S_$plotMapInitSummary()

• DR2S_$plotPartitionSummary()

• DR2S_$plotMapIterSummary()

• DR2S_$plotMapFinalSummary()

• DR2S_$plotRemapSummary()

• DR2S_$plotSeqLogo()

• DR2S_$runMapInit()

• DR2S_$runPartitionLongreads()

• DR2S_$runSplitLongreadsByHaplotype()

• DR2S_$runExtractPartitionedLongreads()

• DR2S_$runMapIter()

• DR2S_$runPartitionShortreads()

• DR2S_$runMapFinal()

• DR2S_$runPipeline()

• DR2S_$clone()

---

Method new()

Create a new DR2S object.

Usage

DR2S_$new(conf, createOutdir = TRUE)

Arguments

conf

A DR2S configuration provided either by [createDR2SConf] or read from file by [readDR2SConf].

createOutdir

Set up the output directory.

Returns

A new DR2S object.

---

Method cache()

Store a DR2S object as an rds file.

Usage

DR2S_$cache(outname)

Arguments

outname

(optional) filename of the stored object.

Returns

Returns invisibly the DR2S object.

---

Method clear()

Clear all the files pertaining to a DR2S mapping process and set up the whole process from scratch.

Usage

DR2S_$clear()

Returns

Returns invisibly the DR2S object.

---

Method cleanup()

remove all bam and bai files.

Usage

DR2S_$cleanup()

Returns

Returns invisibly the DR2S object.

---

Method print()

Print a DR2S object prettily

Usage

DR2S_$print()

Returns

Returns invisibly the DR2S object.

---

Method run_()

Execute a given step in a DR2S pipeline.

Usage

DR2S_$run_(step)

Arguments

step

A step in the DR2S pipeline

Returns

Called for side effect.

---

Method getConfig()

Usage

DR2S_$getConfig(name = NULL)

---

Method setConfig()

Usage

DR2S_$setConfig(name, value)

---

Method getDatadir()

Usage

DR2S_$getDatadir()

---

Method getOutdir()

Usage

DR2S_$getOutdir()

---

Method getMicrosatellite()

Usage

DR2S_$getMicrosatellite()

---

Method getForceMapping()

Usage

DR2S_$getForceMapping()

---

Method getThreshold()

Usage

DR2S_$getThreshold()

---

Method getDistAlleles()

Usage

DR2S_$getDistAlleles()

---

Method getIterations()

Usage

DR2S_$getIterations()

---

Method getLrdMapper()

Usage

DR2S_$getLrdMapper()

---

Method getLrdType()

Usage

DR2S_$getLrdType()

---

Method getLrdDir()

Usage

DR2S_$getLrdDir()

---

Method getLongreads()

Usage

DR2S_$getLongreads()

---

Method getSrdMapper()

Usage

DR2S_$getSrdMapper()

---

Method getSrdType()

Usage

DR2S_$getSrdType()

---

Method getSrdDir()

Usage

DR2S_$getSrdDir()

---

Method getShortreads()

Usage

DR2S_$getShortreads()

---

Method getPipeline()

Usage

DR2S_$getPipeline()

---

Method getOpts()

Usage

DR2S_$getOpts(name = NULL)

---

Method getSampleId()

Usage

DR2S_$getSampleId()

---

Method getLocus()

Usage

DR2S_$getLocus()

---

Method getReference()

Usage

DR2S_$getReference()

---

Method getPlatform()

Usage

DR2S_$getPlatform()

---

Method getFormat()

Usage

DR2S_$getFormat()

---

Method setFormat()

Usage

DR2S_$setFormat(format)

---

Method getDetails()

Usage

DR2S_$getDetails(name = NULL)

---

Method setDetails()

Usage

DR2S_$setDetails(details)

---

Method getSampleDetails()

Usage

DR2S_$getSampleDetails()

---

Method getStats()

Usage

DR2S_$getStats(name = NULL)

---

Method setStats()

Usage

DR2S_$setStats(name, value)

---

Method getLimits()

Usage

DR2S_$getLimits()

---

Method setLimits()

Usage

DR2S_$setLimits(lmts)

---

Method getHapTypes()

Usage

DR2S_$getHapTypes()

---

Method setHapTypes()

Usage

DR2S_$setHapTypes(x)

---

Method getRefPath()

Usage

DR2S_$getRefPath()

---

Method setRefPath()

Usage

DR2S_$setRefPath(refPath)

---

Method getHomozygous()

Usage

DR2S_$getHomozygous()

---

Method setHomozygous()

Usage

DR2S_$setHomozygous(homozygous)

---

Method getRefSeq()

Usage

DR2S_$getRefSeq()

---

Method getPileup()

Usage

DR2S_$getPileup(useSR = FALSE)

---

Method getSnpMatrix()

Usage

DR2S_$getSnpMatrix()

---

Method getPartition()

Usage

DR2S_$getPartition()

---

Method getHapList()

Usage

DR2S_$getHapList(group)

---

Method getLatestRefPath()

Usage

DR2S_$getLatestRefPath()

---

Method getLatestRef()

Usage

DR2S_$getLatestRef()

---

Method getMapTag()

Usage

DR2S_$getMapTag(iter = "init", group = NULL, ref = "LR")

---

Method getGroupPileup()

Usage

DR2S_$getGroupPileup(group = NULL, ref = NULL, iteration = 0)

---

Method getLrdMapFun()

Usage

DR2S_$getLrdMapFun()

---

Method getSrdMapFun()

Usage

DR2S_$getSrdMapFun()

---

Method absPath()

Usage

DR2S_$absPath(filename)

---

Method relPath()

Usage

DR2S_$relPath(filepath)

---

Method hasMapInit()

Usage

DR2S_$hasMapInit()

---

Method hasLrdPartition()

Usage

DR2S_$hasLrdPartition()

---

Method hasHapList()

Usage

DR2S_$hasHapList()

---

Method hasMapIter()

Usage

DR2S_$hasMapIter()

---

Method hasMapFinal()

Usage

DR2S_$hasMapFinal()

---

Method checkGetShortreads()

Usage

DR2S_$checkGetShortreads()

---

Method hasShortreads()

Usage

DR2S_$hasShortreads()

---

Method checkGetLongreads()

Usage

DR2S_$checkGetLongreads()

---

Method hasLongreads()

Usage

DR2S_$hasLongreads()

---

Method plotCoverage()

Usage

DR2S_$plotCoverage(
  threshold,
  range = NULL,
  thin = 0.1,
  width = 1,
  label = "",
  drop.indels = FALSE,
  readtype = "LR"
)

---

Method plotGroupCoverage()

Usage

DR2S_$plotGroupCoverage(
  group = NULL,
  ref = NULL,
  iteration = "init",
  threshold = NULL,
  range = NULL,
  thin = 0.1,
  width = 1,
  label = "",
  drop.indels = FALSE
)

---

Method plotBasecallFrequency()

Usage

DR2S_$plotBasecallFrequency(threshold, label = "", drop.indels = FALSE)

---

Method plotGroupBasecallFrequency()

Usage

DR2S_$plotGroupBasecallFrequency(
  group = NULL,
  ref = NULL,
  iteration = "init",
  threshold = NULL,
  label = "",
  drop.indels = FALSE
)

---

Method plotPartitionHistogram()

Usage

DR2S_$plotPartitionHistogram(label = "", limits = NULL)

---

Method plotPartitionTree()

Usage

DR2S_$plotPartitionTree()

---

Method plotPartitionRadar()

Usage

DR2S_$plotPartitionRadar()

---

Method polymorphicPositions()

Usage

DR2S_$polymorphicPositions(threshold, useSR = FALSE)

---

Method plotMapInitSummary()

Usage

DR2S_$plotMapInitSummary(thin = 0.2, width = 4, label = "")

---

Method plotPartitionSummary()

Usage

DR2S_$plotPartitionSummary(label = "", limits = NULL)

---

Method plotMapIterSummary()

Usage

DR2S_$plotMapIterSummary(
  thin = 0.2,
  width = 10,
  iteration = 0,
  drop.indels = TRUE
)

---

Method plotMapFinalSummary()

Usage

DR2S_$plotMapFinalSummary(readtype, thin = 0.2, width = 10)

---

Method plotRemapSummary()

Usage

DR2S_$plotRemapSummary(readtype, thin = 0.2, width = 10)

---

Method plotSeqLogo()

Usage

DR2S_$plotSeqLogo(ppos = NULL, pwm = NULL)

---

Method runMapInit()

Usage

DR2S_$runMapInit(opts = list(), ...)

---

Method runPartitionLongreads()

Usage

DR2S_$runPartitionLongreads()

---

Method runSplitLongreadsByHaplotype()

Usage

DR2S_$runSplitLongreadsByHaplotype()

---

Method runExtractPartitionedLongreads()

Usage

DR2S_$runExtractPartitionedLongreads()

---

Method runMapIter()

Usage

DR2S_$runMapIter(opts = list(), ...)

---

Method runPartitionShortreads()

Usage

DR2S_$runPartitionShortreads(opts = list(), ...)

---

Method runMapFinal()

Usage

DR2S_$runMapFinal(opts = list(), ...)

---

Method runPipeline()

Usage

DR2S_$runPipeline()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DR2S_$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

DKMS-LSL/dr2s documentation built on March 14, 2021, 2:46 p.m.