/usr/lib/R/site-library/GenABEL/unitTests/runit.impute2xxx.R is in r-cran-genabel 1.7-6-1.
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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 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 | ### --- Test setup ---
if(FALSE) {
## Not really needed, but can be handy when writing tests
library("RUnit")
library("GenABEL")
library("DatABEL")
}
### 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.impute2databel <- function()
{
#library(GenABEL)
#library("RUnit")
unlink("*.fv?")
makedose <- function(prob) {
dose <- 2*prob[c(F,F,T)]+prob[c(F,T,F)]
bp <- prob[c(T,F,F)]
miss <- which((bp+dose)<0.9)
if (length(miss) > 0 ) dose[miss] <- NA
return(dose)
}
makeprob <- function(prob) {
dose2 <- prob[c(F,F,T)]
dose1 <- prob[c(F,T,F)]
bp <- prob[c(T,F,F)]
miss <- which((bp+dose1+dose2)<0.9)
out <- matrix(c(dose2,dose1),ncol=2)
if (length(miss) > 0 ) out[miss,] <- NA
out
}
tmp0 <- read.table("TEST10x15.geno",head=F,strings=F)
snps <- tmp0[,2]
tmp0 <- tmp0[,c(6:dim(tmp0)[2])]
dose <- apply(tmp0,FUN="makedose",MAR=1)
rownames(dose)
prb <- makeprob(tmp0[1,])
for (i in 2:dim(tmp0)[1])
prb <- cbind(prb,makeprob(tmp0[i,]))
dm <- dim(prb)
prb <- as.numeric(prb)
prb <- matrix(prb,ncol=dm[2])
tmp1 <- impute2databel(geno="TEST10x15.geno",
sample="impute.sample5",
out="TEST10x15_T.geno",
makeprob=FALSE,
old=TRUE)
tmp1
tmp1_m <- as(tmp1,"matrix")
tmp1_m
print(tmp0[1:5,1:6])
tmp2 <- impute2databel(geno="TEST10x15.geno",
sample="impute.sample5",
out="TEST10x15_F.geno",
makeprob=TRUE,
old=FALSE)
print(tmp2)
tmp2_m <- as(tmp2,"matrix")
tmp3 <- databel("TEST10x15_F.geno.prob")
tmp3_m <- as(tmp3,"matrix")
checkIdentical(TRUE,all(abs(dose-tmp1_m)<1e-7,na.rm=TRUE))
checkIdentical(TRUE,all(abs(dose-tmp2_m)<1e-7,na.rm=TRUE))
checkIdentical(TRUE,all(abs(prb-tmp3_m)<1e-7,na.rm=TRUE))
checkIdentical(TRUE,all(abs(tmp1_m-tmp2_m)<1e-8,na.rm=TRUE))
checkEqualsNumeric(dose,tmp1_m,checkNames=FALSE,tolerance = 5*(.Machine$double.eps^0.5))
checkEqualsNumeric(dose,tmp2_m,checkNames=FALSE,tolerance = 5*(.Machine$double.eps^0.5))
checkEqualsNumeric(prb,tmp3_m,checkNames=FALSE,tolerance = 5*(.Machine$double.eps^0.5))
checkIdentical(tmp1_m,tmp2_m)
checkEqualsNumeric(tmp1_m,tmp2_m)
smpl <- read.table("impute.sample5",head=F,skip=2,strings=F)[,1]
rownames(dose) <- smpl
rownames(prb) <- smpl
checkEquals(dose,tmp1_m,tolerance=4*sqrt(.Machine$double.eps))
checkEquals(dose,tmp2_m,tolerance=4*sqrt(.Machine$double.eps))
checkEquals(prb,tmp3_m,tolerance=4*sqrt(.Machine$double.eps))
checkIdentical(tmp1_m,tmp2_m)
checkEqualsNumeric(tmp1_m,tmp2_m)
checkIdentical(rownames(tmp1),smpl)
checkIdentical(rownames(tmp2),smpl)
checkIdentical(rownames(tmp3),smpl)
checkIdentical(dimnames(tmp1),dimnames(tmp1_m))
checkIdentical(dimnames(tmp2),dimnames(tmp2_m))
checkIdentical(dimnames(tmp3),dimnames(tmp3_m))
checkIdentical(get_dimnames(tmp1),list(smpl,snps))
checkIdentical(get_dimnames(tmp2),list(smpl,snps))
snps2 <- rep(0,2*length(snps))
snps2[c(T,F)] <- paste(snps,"_11",sep="")
snps2[c(F,T)] <- paste(snps,"_01",sep="")
checkIdentical(get_dimnames(tmp3),list(smpl,snps2))
rm(list=ls());gc()
unlink("*.fv?")
}
# fixing CRAN NOTE
#
test.SNPquoted <- function() {
#library("RUnit")
#library("GenABEL")
require(DatABEL)
# generate some random data in "prob" format
Nids <- 10
Nsnps <- 3
q <- runif(Nsnps,min=0.2,max=0.8)
PROB0 <- apply(matrix(q,ncol=1),MARGIN=1,FUN=function(x){
cBB <- rnorm(Nids,mean=x^2,sd=0.01)
cAB <- rnorm(Nids,mean=2*x*(1-x),sd=0.01)
cAA <- 1-cBB-cAB
cAA <- matrix(cAA,ncol=1)
return(c(cAA,cAB,cBB))
})
PROB <- matrix(NA,ncol=3*Nsnps,nrow=Nids)
for (i in 1:Nsnps) {
for (j in 1:3) {
PROB[,(i-1)*3+j] <- PROB0[c(((j-1)*Nids+1):(j*Nids)),i]
}
}
daProb <- matrix2databel(t(PROB),filename="temp_daProb")
# conversion functions
makedose <- function(prob) {
dose <- 2*prob[c(F,F,T)]+prob[c(F,T,F)]
bp <- prob[c(T,F,F)]
miss <- which(abs(bp)<1e-16 & abs(dose)<1e-16)
if (length(miss) > 0 ) dose[miss] <- NA
return(dose)
}
pfun <- function(a) return(a)
dosefile <- apply2dfo(dfodata=daProb, anFUN = "makedose",
MAR = 2, procFUN = "pfun",prob=get("SNP"),
outclass="databel",
outfile="temp_myTestDose",
type="DOUBLE",transpose=FALSE)
# check equality
DOSE <- matrix(NA,ncol=Nids,nrow=Nsnps)
for (i in 1:Nids) for (j in 1:Nsnps) {
DOSE[j,i] <- 2*PROB[i,j*3]+PROB[i,j*3-1]
}
checkEqualsNumeric(DOSE,as(dosefile,"matrix"))
rm(dosefile); gc()
unlink("temp_myTestDose.fv?")
rm(daProb); gc()
unlink("temp_daProb.fv?")
}
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