calls {crlmm}R Documentation

Accessors for Calls and Confidences on a SnpSet object

Description

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

confs returns the confidences associated to the genotype calls. THe current implementation of CRLMM stores the confidences as integers by using the transformation:

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

where 'p' is the posterior probability of the call.

Usage

calls(x)
confs(x)

Arguments

x SnpSet object

Value

Matrix of genotype calls or confidences.

Examples

  set.seed(1)
  theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)
  p <- matrix(runif(20), nc=2)
  theConfs <- round(-1000*log2(1-p))
  obj <- new("SnpSet", call=theCalls, callProbability=theConfs)
  calls(obj)
  confs(obj)

[Package crlmm version 1.2.4 Index]