oligoClasses (version 1.34.0)

SnpSet-methods: Accessors and methods for SnpSet objects

Description

Utility functions for accessing data in SnpSet objects.

Usage

calls(object)
calls(object) <- value
confs(object, transform=TRUE)
confs(object) <- value

Arguments

object

A SnpSet object.

transform

Logical. Whether to transform the integer representation of the confidence score (for memory efficiency) to a probability. See details.

value

A matrix.

Details

calls returns the genotype calls. CRLMM stores genotype calls as integers (1 - AA; 2 - AB; 3 - BB).

confs returns the confidences associated with the genotype calls. The current implementation of CRLMM stores the confidences as integers to save memory on disk by using the transformation:

round(-1000*log2(1-p)),

where 'p' is the posterior probability of the call. confs is a convenience function that transforms the integer representation back to a probability. Note that if the assayData elements of the SnpSet objects are ff_matrix or ffdf, the confs function will return a warning. For such objects, one should first subset the ff object and coerce to a matrix, then apply the above conversion. The function snpCallProbability for the callProbability slot of SnpSet objects. See the examples below.

checkOrder checks whether the object is ordered by chromosome and physical position, evaluating to TRUE or FALSE.

See Also

The helper functions p2i converts probabilities to integers and i2p converts integers to probabilities.

See order and checkOrder.

Examples

	theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)
	p <- matrix(runif(20), nc=2)
	integerRepresentation <- matrix(as.integer(round(-1000*log(1-p))), 10, 2)
	obj <- new("SnpSet2", call=theCalls, callProbability=integerRepresentation)
	calls(obj)
        confs(obj)  ## coerces to probability scale
        int <- Biobase::snpCallProbability(obj) ## not necessarily a probability
        p3 <- i2p(int)  ## to convert back to a probability