AllelicImbalance (version 1.10.2)

lva: lva

Description

make an almlof regression for arrays

Usage

lva(x, ...)
"lva"(x, rv, region, settings = list(), return.class = "LinkVariantAlmlof", verbose = FALSE, ...)

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)

verbose

logical, if set TRUE, then function will be more talkative

Details

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

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)