DR2S_: Class '"DR2S"'

In gschofl/DR2S: Dual redundant reference sequencing

Description

Class "DR2S"

Usage

InitDR2S(config, createOutdir = TRUE)

Format

An object of class R6ClassGenerator of length 24.

Value

Object of R6Class representing a DR2S analysis.

Fields

InitDR2S

Initialize DR2S from a config.

mapInit

[MapList]; the mapping of long reads to reference.

partition

[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.

mapFinal

[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.

Public Methods

x$runMapInit( opts = list(), createIgv = TRUE, plot = TRUE, ...)

Run the inital mapping step (long reads against the reference allele)

x$runPartitionLongreadsplot = TRUE, ...)

Partition mapped longreads into haplotypes

x$runSplitLongreadsByHaplotype((plot = TRUE)

Partition mapped longreads into haplotypes

x$runExtractPartitionedLongreads()

Extract FASTQs for partitioned reads.

Internals

x$new(conf, createOutdir = TRUE)

Initialise object of class DR2S.

x$getConfig(name = NULL

Extract configuration

x$setConfig(name, value

Modify configuration

gschofl/DR2S documentation built on May 17, 2019, 8:40 a.m.