/usr/lib/R/site-library/GenABEL/unitTests/runit.recodeChromosome.R is in r-cran-genabel 1.7-6-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | ### --- Test setup ---
#
# regression test
#
if(FALSE) {
## Not really needed, but can be handy when writing tests
library(RUnit)
library(GenABEL)
}
### do not run
#stop("SKIP THIS TEST")
###
### ---- common functions and data -----
#source(paste("../inst/unitTests/shared_functions.R"))
#source(paste(path,"/shared_functions.R",sep=""))
### --- Test functions ---
test.recodeChromosome <- function()
{
data(ge03d2ex)
lst <- list("3"="X","2"=15)
dta0 <- chromosome(recodeChromosome(ge03d2ex,lst))
dta1 <- chromosome(recodeChromosome(gtdata(ge03d2ex),lst))
qts <- qtscore(dm2,ge03d2ex)
dta2 <- chromosome(recodeChromosome(qts,lst))
checkIdentical(dta0,dta1)
checkIdentical(dta0,dta2)
checkException( dta <- recodeChromosome(10,lst) )
checkException( dta <- recodeChromosome(ge03d2ex,c(10,12)) )
lst <- list("1"="X","1"="Y")
checkException( dta <- recodeChromosome(ge03d2ex,lst) )
lst <- list("1"="2","2"="3")
checkException( dta <- recodeChromosome(ge03d2ex,lst) )
lst <- list("1"="oppa","2"=c(1,2))
checkException( dta <- recodeChromosome(ge03d2ex,lst) )
lst <- list("1"="0","2"=c())
checkException( dta <- recodeChromosome(ge03d2ex,lst) )
}
|