UR: UR object

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

UR object

Description

Class for storing RA data and associated functions for analysis of unrelated populations.

Usage

URobj <- makeUR(RAobj, ploid = 2,indsubset = NULL, filter = list(MAF = 0.01,
  MISS = 0.5, HW = c(-0.05, Inf), MAXDEPTH = 500), mafEst = TRUE,
  nThreads = 2)

Details

An UR object is created from the makeUR function and contains RA data, various statistics of the dataset that have been computed, and functions (or methods) for analyzing the data. Information in an UR object are specific to unrelated populations (or populations with no known relationships).

Super class

GUSbase::RA -> UR

Methods

Public methods

• UR$new()

• UR$clone()

Inherited methods

• GUSbase::RA$RDDPlot()
• GUSbase::RA$cometPlot()
• GUSbase::RA$extractVar()
• GUSbase::RA$mergeSamples()
• GUSbase::RA$print()
• GUSbase::RA$rocketPlot()
• GUSbase::RA$writeRA()
• GUSbase::RA$writeVCF()

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Method new()

Usage

UR$new(R6obj, ploid)

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Method clone()

The objects of this class are cloneable with this method.

Usage

UR$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Author(s)

Timothy P. Bilton

See Also

makeUR

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