Utility functions for accessing data in
1 2 3 4
A SnpSet object.
Logical. Whether to transform the integer representation of the confidence score (for memory efficiency) to a probability. See 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:
where 'p' is the posterior probability of the call.
a convenience function that transforms the integer representation
back to a probability. Note that if the assayData elements of the
SnpSet objects are
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.
Note that the replacement method for
confs<- expects a matrix
of probabilities and will automatically convert the probabilities to
an integer representation. See details for the conversion.
snpCallProbability is an accessor for the
'callProbability' element of the
assayData. The name can be
misleading, however, as the accessor will not return a probability if
the call probabilities are represented as integers.
1 2 3 4 5 6 7 8
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.