inst/tests/tests.R

In chr1swallace/snpBMA: BMA exploration of multi-SNP models in genetic association testing

## load sample data
##context("prep\n")
data(for.exercise, package="snpStats")
test.data <- snps.10[,101:110]
cs <- col.summary(test.data)
tags <- tag(test.data, 0.9)
w <- sqrt(0.5)
mn <- as(test.data[,1],"numeric")
y <- rnorm(nrow(test.data),mean=ifelse(is.na(mn),0,mn),sd=w) + rnorm(nrow(test.data),sd=sqrt(0.5))
stratum <- sample(rep(1:2, length.out=length(y)))

## tagging
context("tagging\n")
test_that("tag finds the right number of tags", {
  expect_equal(length(unique(tag(X=test.data,tag.threshold=0.5))), 3)
})

## make.group
## test_that("make.group checks parameters", {
##   expect_that( make.group(-1), throws_error())
##   expect_that( make.group(1.1), throws_error())
## })

## do.merge
## groups <- list(a=c("a","b","c"),
##                d=c("d","e","f"),
##                g=c("g","h"))
## test_that("do.merge works", {
##   expect_equal( length(do.merge(groups, c("a","d"))), 2)
##   expect_that( do.merge(groups, c("a","e")), throws_error())
## })
          
################################################################################

## l.rbind/ l.c
context("l.rbind/l.c\n")

test_that("l.c works", {
  test.list <- list(list(A=list(a=1:2,b=3:5)),
                    list(A=list(a=11:15,b=21:28)))
  expect_identical(l.c( test.list, "A", "b" ), 
                   c(3:5,21:28))
})

test_that("l.rbind works", {
  test.list2 <- list(list(A=list(a=matrix(1:4,2,2))),
                     list(A=list(a=matrix(5:10,3,2))))
  expect_identical(l.rbind( test.list2, "A", "a" ), 
                   rbind(matrix(1:4,2,2), matrix(5:10,3,2)))
})

################################################################################

## stratification
context("stratification")
data <- make.data(X=test.data, Y=y, tags=tags, family="gaussian")
sdata <- make.data(X=test.data, Y=y, tags=tags, family="gaussian", strata=stratum)

bma.nsnps(data, nsnps=1)
bma.nsnps(sdata, nsnps=1)