lva.internal: lva.internal

In AllelicImbalance: Investigates Allele Specific Expression

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)

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.