data(ASEset)
a <- ASEset
# Add phase
set.seed(1)
p1 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
p2 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
p <- matrix(paste(p1,sample(c("|","|","/"), size=nrow(a)*ncol(a), replace=TRUE), p2, sep=""),
nrow=nrow(a), ncol(a))
phase(a) <- p
#add alternative allele information
mcols(a)[["alt"]] <- inferAltAllele(a)
# in this example two overlapping subsets of snps in the ASEset defines the region
region <- split(granges(a)[c(1,2,2,3)], c(1,1,2,2))
rs <- regionSummary(a, region, return.class="array", return.meta=FALSE)
# use (change to generated riskSNP phase later)
phs <- array(c(phase(a,return.class="array")[1,,c(1, 2)],
phase(a,return.class="array")[2,,c(1, 2)]), dim=c(20,2,2))
grp <- matrix(2, nrow=dim(phs)[1], ncol=dim(phs)[2])
grp[(phs[,,1] == 0) & (phs[,,2] == 0)] <- 1
grp[(phs[,,1] == 1) & (phs[,,2] == 1)] <- 3
#only use mean.fr at the moment, which is col 3
lva.internal(assays(rs)[["rs1"]], grp, 3)
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