Raw coding of posterior probabilities of SNP genotype
An uncertain SNP genotype call is represented by the three posterior
probabilities of the three possible calls. In the class
SnpMatrix, an approximation to these is packed into a single
1-byte variable of type raw. These functions carry out this coding (and
decoding).
post2g(p, transpose = FALSE) mean2g(m, maxE = FALSE) g2post(g, transpose = FALSE)
p |
A matrix of posterior probabilities. If |
m |
A vector of posterior means |
g |
A |
transpose |
A logical flag indicating transposition of the matric of posterior probabilities (see Description) |
maxE |
A logical flag selecting the maximum entropy option in
|
post2g and g2post convert from posterior probabilities to
raw code and back respectively. If only the posterior expectation
of the genotype (when numerically coded 0, 1, or 2) is available, no
unique soultion exists in general and the behaviour of the function is
determined by the value of maxE. If TRUE, then the maximum
entropy solutions are returned while, if FALSE, an attempt is made
to return the least uncertain solution, by setting the posterior
probability of the BB genotype to zero when the posterior mean is
less than 1.0 and the probability of AA to zero when the mean is
greater than 1.0.
post2g and mean2g return a vector of type
raw. g2post returns a numeric matrix.
These functions are provided mainly for users wishing to write their own data input functions.
David Clayton dc208@cam.ac.uk
data(testdata) g <- Autosomes[1:10, 20] ## A vector of codes p <- g2post(g) ## Transform to probabilities ... pg <- post2g(p) ## ... and back to codes m <- p[,2]+2*p[,3] ## Posterior expectations mg <- mean2g(m) ## Transform to codes ... pmg <- g2post(mg) ## ... and transform to probabilities ## Write everything out print(cbind(as(g, "numeric"), p, as.numeric(pg), m, as.numeric(mg), pmg))
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