DKMS-LSL/dr2s
Dual redundant reference sequencing

Package index
Search the DKMS-LSL/dr2s package
Vignettes
Functions
417
Source code
36
Man pages
57
Home
/
GitHub
/
DKMS-LSL/dr2s
/
DR2S_: R6 Class '"DR2S"'

DR2S_: R6 Class '"DR2S"'
In DKMS-LSL/dr2s: Dual redundant reference sequencing

Description Public fields Methods

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

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.

Related to DR2S_ in DKMS-LSL/dr2s...

DKMS-LSL/dr2s index
README.md

R Package Documentation

rdrr.io home R language documentation Run R code online

Browse R Packages

CRAN packages Bioconductor packages R-Forge packages GitHub packages

We want your feedback!

Note that we can't provide technical support on individual packages. You should contact the package authors for that.
GitHub issue tracker
ian@mutexlabs.com
Personal blog

 
Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.

Close