lva.internal {AllelicImbalance} | R Documentation

## lva.internal

### Description

make an almlof regression for arrays (internal function)

### Usage

    lva.internal(x, ...)

    ## S4 method for signature 'array'
    lva.internal(
      x,
      grp,
      element = 3,
      type = "lm",
      subject = NULL,
      covariates = matrix(),
      ...
    )

### Arguments

`x` | regionSummary array phased for maternal allele
`...` | arguments to forward to internal functions
`grp` | group 1-3 (1 for 0:0, 2 for 1:0 or 0:1, and 3 for 1:1)
`element` | which column in x contains the values to use with lm.
`type` | which column in x contains the values to use with lm.
`subject` | which samples belongs to the same individual
`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). Input and output objects can change format slightly in future.

### 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)

    # 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(x=assays(rs)[["rs1"]],grp=grp, element=3)

[Package AllelicImbalance version 1.30.0 Index]