callEmission {VanillaICE} | R Documentation |
When confidence estimates are incorporated in the ICE HMM for genotype calls, the observed data at a SNP is the genotype call and the uncertainty measure. The joint distribution of the call and the uncertainty measure depends on the underlying hidden state. This function calculates the emission probability for the joint sequence of calls and confidence scores. See reference for additioal details.
callEmission(object, P.CHOM.Normal, P.CHOM.LOH, SAMPLE=1)
object |
An object inheriting from AnnotatedSnpSet |
P.CHOM.Normal |
probability of called homozygous given the true underlying state is normal (retention of heterozygosity) |
P.CHOM.LOH |
probability of called homozygous given the true underlying state is loss of heterozygosity |
SAMPLE |
Integer: which sample |
This function is essentially a wrapper for
getHapmapProbabilities
that allows the object to contain the
merged 50k Xba and Hind chips, or the merged 250k Nsp and Sty chips.
Because the distribution of the uncertainty estimates are
chip-specific (enzyme-specific), this function computes
enzyme-specific emission probabilities (note: one of the columns in
featureData
must have the name 'enzyme' and the elements in
the vector must be 'Xba' and 'Hind' or 'Nsp' and 'Sty'.).
The annotation slot in the object must contain one of the following strings that identifies the Affymetrix chip:
mapping100k (if the 50k xba and 50k hind results have been merged into one object)
pd.mapping50k.xba240 (50k Xba platform)
pd.mapping50k.hind240 (50k Hind)
mapping500k (if the two 250k chips – Nsp and Sty – have been merged)
pd.mapping250k.nsp
pd.mapping250k.sty
getHapmapProbabilities
, crlmm
,
featureData
For the callsConfidence package, see
http://www.biostat.jhsph.edu/~rscharpf/software/index.html
data(chromosome1) ##Create an object of class AnnotatedSnpCallSet callset <- new("AnnotatedSnpSet", calls=calls(chromosome1), callsConfidence=callsConfidence(chromosome1), featureData=featureData(chromosome1), phenoData=phenoData(chromosome1), annotation=annotation(chromosome1)) ##1 = homozygous (AA or BB), 2 = heterozygous calls(callset)[calls(callset) == 3] <- 1 ##make sure that enzyme information is stored in featureData ## Not run: require("callsConfidence") emissionProb <- callEmission(object=callset, P.CHOM.Normal=0.70, P.CHOM.LOH=0.999) range(emissionProb) ## End(Not run)