Hi,
Does anybody know how to obtain the imputed SNP genotype probabilities from the
snpStats package?
I am interested in using an imputation method implemented in R to be further
used in a simulation study context.
I have found the snpStats package that seems to contain suitable functions to do
so.
As far as I could find out from the package vignette examples and its help, it
gives the 'dosage' as the output which is the expected number of risk
alleles as a single value. However I need the 3 genotype probabilities (the
probability of having 0, 1 and 2 risk allele copies) and not the
'dosage'. I couldn't find out how to obtain these probabilities.
To illustrate this, here is the code from the snpStats vignette:
##### snpStats vignette example ###
library(snpStats)
library(hexbin)
data(for.exercise)
training <- sample(1000, 200)
select <- seq(1, ncol(snps.10), 2)
missing <- snps.10[training, select]
present <- snps.10[training, -select]
target <- snps.10[-training, -select]
lost <- snps.10[-training, select]
pos.miss <- snp.support$position[select]
pos.pres <- snp.support$position[-select]
rules <- snp.imputation(present, missing, pos.pres, pos.miss)
imputed <- impute.snps(rules, target, as.numeric = FALSE)
########
The 'imputed' object stores the imputed SNP, but it contains the dosage
or the genotypes but under 'raw' class, and I don't know how to
extract the genotype probabilities from this object.
Thanks in advance.
Isaac Subirana.
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