LinkVariantAlmlof-plot {AllelicImbalance} | R Documentation |
plot an object of type LinkVariantAlmlof
plot(x, y, ...) ## S4 method for signature 'LinkVariantAlmlof,ANY' plot(x, y, ...)
x |
LinkVariantAlmlof object |
y |
not used |
... |
pass on arguments to internal methods |
Jesper R. Gadin, Lasse Folkersen
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) #init risk variants p.ar <- phaseMatrix2Array(p) rv <- RiskVariantFromGRangesAndPhaseArray(x=GRvariants, phase=p.ar) #colnames has to be samea and same order in ASEset and RiskVariant colnames(a) <- colnames(rv) # in this example each and every snp in the ASEset defines a region r1 <- granges(a) # in this example two overlapping subsets of snps in the ASEset defines the region r2 <- split(granges(a)[c(1,2,2,3)],c(1,1,2,2)) # link variant almlof (lva) lv1 <- lva(a, rv, r1) lv2 <- lva(a, rv, r2) plot(lv2[1])