LinkVariantAlmlof-plot {AllelicImbalance} | R Documentation

## plot LinkVariantAlmlof objects

### Description

plot an object of type LinkVariantAlmlof

### Usage

    plot(x, y, ...)

    ## S4 method for signature 'LinkVariantAlmlof,ANY'
    plot(x, y, ...)

### Arguments

`x` | LinkVariantAlmlof object
`y` | not used
`...` | pass on arguments to internal methods

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### Examples

    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])

[Package AllelicImbalance version 1.20.0 Index]