calls {crlmm} | R Documentation |
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.
calls(x) confs(x)
x |
SnpSet object |
Matrix of genotype calls or confidences.
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)