RA: RA Object

In tpbilton/GUSbase: Genotyping Uncertainty with Sequencing Data: Base Package

RA Object

Description

Class for storing reference/alternative (RA) data and methods for performing exporartory data analysis on sequencing data.

Usage

## Create RA object
RAobj <- readRA(rafile, snpsubset=NULL, sampthres = 0.01, excsamp = NULL)

## RA Functions (Methods)
RAobj$extractVar(nameList)
RAobj$mergeSamples(samID, useID=TRUE)
RAobj$writRA(snpsubset=NULL, indsubset=NULL, file="GUSbase")
RAobj$writeVCF(snpsubset=NULL, indsubset=NULL, file="GUSbase", IDuse=NULL)

Details

An RA object is returned from the readRA function and contains the RA data, various statistics of the dataset that have been computed, and functions (or methods) for analyzing the data.

Methods (Functions)

A list of the methods that are available to an RA object:

$extractVar

Extract private variables stored in an RA object

$mergeSamples

Merge read counts for different samples

$writeRA

Convert the data in the RA object back to an RA file

$writeVCF

Convert the data in the RA object back to VCF format

Methods

Public methods

• RA$new()

• RA$print()

• RA$mergeSamples()

• RA$extractVar()

• RA$cometPlot()

• RA$rocketPlot()

• RA$RDDPlot()

• RA$writeVCF()

• RA$writeRA()

• RA$clone()

---

Method new()

Usage

RA$new(List)

---

Method print()

Usage

RA$print(...)

---

Method mergeSamples()

Usage

RA$mergeSamples(samID, useID = TRUE)

---

Method extractVar()

Usage

RA$extractVar(nameList)

---

Method cometPlot()

Usage

RA$cometPlot(
  ploid = 2,
  filename = NULL,
  cex = 1,
  maxdepth = 500,
  maxSNPs = 1e+06,
  res = 300,
  ind = FALSE,
  ncores = 1,
  ...
)

---

Method rocketPlot()

Usage

RA$rocketPlot(
  ploid = 2,
  filename = NULL,
  cex = 1,
  maxdepth = 500,
  maxSNPs = 1e+05,
  res = 300,
  scaled = TRUE,
  ...
)

---

Method RDDPlot()

Usage

RA$RDDPlot(ploid = 2, filename = NULL, maxdepth = 500, maxSNPs = 1e+05, ...)

---

Method writeVCF()

Usage

RA$writeVCF(snpsubset = NULL, indsubset = NULL, file = "GUSbase", IDuse = NULL)

---

Method writeRA()

Usage

RA$writeRA(snpsubset = NULL, indsubset = NULL, file = "GUSbase")

---

Method clone()

The objects of this class are cloneable with this method.

Usage

RA$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Author(s)

Timothy P. Bilton

See Also

readRA

tpbilton/GUSbase documentation built on March 8, 2024, 1:35 p.m.