lva {AllelicImbalance} | R Documentation

## lva

### Description

make an almlof regression for arrays

### Usage

    lva(x, ...)

    ## S4 method for signature 'ASEset'
    lva(
      x,
      rv,
      region,
      settings = list(),
      return.class = "LinkVariantAlmlof",
      type = "lm",
      verbose = FALSE,
      covariates = matrix(),
      ...
    )

### Arguments

`x` | ASEset object with phase and 'ref'/'alt' allele information
`...` | arguments to forward to internal functions
`rv` | RiskVariant object with phase and 'ref'/'alt' allele information
`region` | RiskVariant object with phase and alternative allele information
`settings` | RiskVariant object with phase and alternative allele information
`return.class` | 'LinkVariantAlmlof' (more options in future)
`type` | "lm" or "nlme", "nlme" needs subject information
`verbose` | logical, if set TRUE, then function will be more talkative
`covariates` | add data.frame with covariates (only integers and numeric)

### Details

internal method that takes one array with results from regionSummary and one matrix with group information for each risk SNP (based on phase)

### 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)

    #use GRangesList to merge and use regions defined by each element of the
    #GRangesList
    r1b <- GRangesList(r1)
    r1c <- GRangesList(r1, r1)

    # 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)
    lva(a, rv, r1)
    lva(a, rv, r1b)
    lva(a, rv, r1c)
    lva(a, rv, r2)

    # Use covariates (integers or nuemric)
    cov <- data.frame(age=sample(20:70, ncol(a)), sex=rep(c(1,2), each=ncol(a)/2),
    row.names=colnames(a))
    lva(a, rv, r1, covariates=cov)
    lva(a, rv, r1b, covariates=cov)
    lva(a, rv, r1c, covariates=cov)
    lva(a, rv, r2, covariates=cov)

    # link variant almlof (lva), using nlme
    a2 <- a
    ac <- assays(a2)[["countsPlus"]]
    jit <- sample(c(seq(-0.10,0,length=5), seq(0,0.10,length=5)), size=length(ac) , replace=TRUE)
    assays(a2, withDimnames=FALSE)[["countsPlus"]] <- round(ac * (1+jit),0)
    ab <- cbind(a, a2)
    colData(ab)[["subject.group"]] <- c(1:ncol(a),1:ncol(a))
    rv2 <- rv[,c(1:ncol(a),1:ncol(a))]
    colnames(ab) <- colnames(rv2)

    lva(ab, rv2, r1, type="nlme")
    lva(ab, rv2, r1b, type="nlme")
    lva(ab, rv2, r1c, type="nlme")
    lva(ab, rv2, r2, type="nlme")

[Package AllelicImbalance version 1.25.2 Index]