AssayData-methods: Methods for class AssayData in the oligoClasses package

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

Batch statistics used for estimating copy number are stored as AssayData in the 'batchStatistics' slot of the CNSet class. Each element in the AssayData must have the same number of rows and columns. Rows correspond to features and columns correspond to batch.

Objects from the Class

A virtual Class: No objects may be created from it.

Methods

batchNames

signature(object = "AssayData"): ...

batchNames<-

signature(object = "AssayData"): ...

corr

signature(object = "AssayData", allele = "character"): ...

nu

signature(object = "AssayData", allele = "character"): ...

phi

signature(object = "AssayData", allele = "character"): ...

Details

lM: Extracts entire list of linear model parameters.

corr: The within-genotype correlation of log2(A) and log2(B) intensities.

nu: The intercept for the linear model. The linear model is fit to the A and B alleles independently.

phi: The slope for the linear model. The linear model is fit independently to the A and B alleles.

See Also

CNSet-class

Examples

library(crlmm)
library(Biobase)
data(cnSetExample, package="crlmm")
cnSet <- cnSetExample
isCurrent(cnSet)
assayDataElementNames(batchStatistics(cnSet))
## Accessors for linear model parameters
## -- Included here primarily as a check that accessors are working
## -- Values are all NA until CN estimation is performed using the crlmm package
##
## subsetting
cnSet[1:10, ]
## names of elements in the object
## accessors for parameters
nu(cnSet, "A")[1:10, ]
nu(cnSet, "B")[1:10, ]
phi(cnSet, "A")[1:10, ]
phi(cnSet, "B")[1:10, ]

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.