GenotypeData_test.R
In GWASTools: Tools for Genome Wide Association Studies

test_GenotypeData <- function() {
  # simulate data
  ncfile <- tempfile()
  simulateGenotypeMatrix(n.snps=10, n.chromosomes=26,
                         n.samples=20, filename=ncfile, file.type="ncdf")
  nc <- NcdfGenotypeReader(ncfile)
  scanID <- getScanID(nc)
  sex <- c(rep("M", 10), rep("F", 10))
  plate <- rep(paste("batch", 1:4, sep=""), 5)
  scandf <- data.frame(scanID=scanID, sex=sex, plate=plate)
  scanAnnot <- ScanAnnotationDataFrame(scandf)
  snpID <- getSnpID(nc)
  chrom <- getChromosome(nc)
  pos <- getPosition(nc)
  rsID <- paste("rs", snpID, sep="")
  snpdf <- data.frame(snpID=snpID, chromosome=chrom, position=pos, rsID=rsID,
                      stringsAsFactors=FALSE)
  snpAnnot <- SnpAnnotationDataFrame(snpdf)

  # creation with only ncdf
  obj <- GenotypeData(nc)
  checkTrue(!hasSnpAnnotation(obj))
  checkTrue(!hasScanAnnotation(obj))
  checkIdentical(getSnpAnnotation(obj), NULL)
  checkIdentical(getScanAnnotation(obj), NULL)
  # creation with only snpAnnot
  obj <- GenotypeData(nc, snpAnnot=snpAnnot)
  checkTrue(hasSnpAnnotation(obj))
  checkTrue(!hasScanAnnotation(obj))
  checkIdentical(getSnpAnnotation(obj), snpAnnot)
  # creation with only scanAnnot
  obj <- GenotypeData(nc, scanAnnot=scanAnnot)
  checkTrue(!hasSnpAnnotation(obj))
  checkTrue(hasScanAnnotation(obj))
  checkIdentical(getScanAnnotation(obj), scanAnnot)
  # creation with both annotations
  obj <- GenotypeData(nc, snpAnnot=snpAnnot, scanAnnot=scanAnnot)
  checkTrue(hasSnpAnnotation(obj))
  checkTrue(hasScanAnnotation(obj))
  checkIdentical(getScanAnnotation(obj), scanAnnot)
  checkIdentical(getSnpAnnotation(obj), snpAnnot)
  
  # required variables
  geno <- getGenotype(obj)
  checkIdentical(c(nsnp(obj),nscan(obj)), dim(geno))
  checkIdentical(length(getSnpID(obj)), nsnp(obj))
  checkIdentical(length(getChromosome(obj)), nsnp(obj))
  checkIdentical(length(getPosition(obj)), nsnp(obj))
  checkIdentical(length(getScanID(obj)), nscan(obj))

  # annotation variables - snp
  checkTrue(is.character(getSnpVariableNames(obj)))
  checkTrue(hasSnpVariable(obj, "rsID"))
  checkTrue(!hasSnpVariable(obj, "foo"))
  checkIdentical(NULL, getSnpVariable(obj, "foo"))
  # annotation variables - scan
  checkTrue(is.character(getScanVariableNames(obj)))
  checkTrue(hasSex(obj))
  checkTrue(hasScanVariable(obj, "plate"))
  checkTrue(!hasScanVariable(obj, "foo"))
  checkIdentical(NULL, getScanVariable(obj, "foo"))

  # annotation mismatch
  snpAnnot <- snpAnnot[1:100,]
  checkException(GenotypeData(nc, snpAnnot=snpAnnot))
  scanAnnot$scanID[1] <- 25L
  checkException(GenotypeData(nc, scanAnnot=scanAnnot))

  close(obj)
  unlink(ncfile)
}

test_GenotypeData_Gds <- function() {
  file <- tempfile()
  gds <- createfn.gds(file)
  snp <- 1:260
  chrom <- rep(1:26, each=10)
  pos <- rep(1001:1026, 10)
  samp <- 1231:1235
  nsnp <- length(snp)
  nsamp <- length(samp)
  geno <- matrix(sample(0:3, nsnp*nsamp, replace=TRUE),
                 nrow=nsnp, ncol=nsamp)
  add.gdsn(gds, "snp.id", snp)
  add.gdsn(gds, "snp.chromosome", chrom)
  add.gdsn(gds, "snp.position", pos)
  add.gdsn(gds, "sample.id", samp)
  add.gdsn(gds, "genotype", geno, storage="bit2")
  closefn.gds(gds)

  snpAnnot <- SnpAnnotationDataFrame(data.frame(snpID=snp, chromosome=chrom, position=pos))
  scanAnnot <- ScanAnnotationDataFrame(data.frame(scanID=samp))
  gdsobj <- GdsGenotypeReader(file)
  obj <- GenotypeData(gdsobj, snpAnnot=snpAnnot, scanAnnot=scanAnnot)
  geno[geno == 3] <- NA
  checkIdentical(geno, getGenotype(obj))
  checkIdentical(snp, getSnpID(obj))
  checkIdentical(chrom, getChromosome(obj))
  checkIdentical(pos, getPosition(obj))
  checkIdentical(samp, getScanID(obj))

  close(obj)
  unlink(file)
}

test_GenotypeData_Matrix <- function() {
  snp <- 1:260
  chrom <- rep(1:26, each=10)
  pos <- rep(1001:1026, 10)
  samp <- 1231:1235
  nsnp <- length(snp)
  nsamp <- length(samp)
  geno <- matrix(sample(c(0,1,2,NA), nsnp*nsamp, replace=TRUE),
                 nrow=nsnp, ncol=nsamp)
  mgr <- MatrixGenotypeReader(genotype=geno, snpID=snp, chromosome=chrom, position=pos, scanID=samp)

  snpAnnot <- SnpAnnotationDataFrame(data.frame(snpID=snp, chromosome=chrom, position=pos))
  scanAnnot <- ScanAnnotationDataFrame(data.frame(scanID=samp))
  obj <- GenotypeData(mgr, snpAnnot=snpAnnot, scanAnnot=scanAnnot)
  checkIdentical(geno, getGenotype(obj))
  checkIdentical(snp, getSnpID(obj))
  checkIdentical(chrom, getChromosome(obj))
  checkIdentical(pos, getPosition(obj))
  checkIdentical(samp, getScanID(obj))
}

test_GenotypeData_char <- function() {
  snp <- 1:260
  chrom <- rep(1:26, each=10)
  pos <- rep(1001:1026, 10)
  A <- rep("G", length(snp))
  B <- rep("C", length(snp))
  samp <- 1231:1235
  nsnp <- length(snp)
  nsamp <- length(samp)
  geno <- matrix(sample(c(0,1,2,NA), nsnp*nsamp, replace=TRUE),
                 nrow=nsnp, ncol=nsamp)
  mgr <- MatrixGenotypeReader(genotype=geno, snpID=snp, chromosome=chrom, position=pos, scanID=samp
)
  snpAnnot <- SnpAnnotationDataFrame(data.frame(snpID=snp, chromosome=chrom, position=pos,
                                                stringsAsFactors=FALSE))
  obj <- GenotypeData(mgr, snpAnnot=snpAnnot)
  gc <- getGenotype(obj, char=TRUE)
  checkTrue(all(gc %in% c(NA,"A/A","A/B","B/B")))
  checkIdentical(is.na(geno), is.na(gc))
  checkIdentical(geno == 0, gc == "B/B")
  checkIdentical(geno == 1, gc == "A/B")
  checkIdentical(geno == 2, gc == "A/A")
  
  snpAnnot$alleleA <- A
  snpAnnot$alleleB <- B
  obj <- GenotypeData(mgr, snpAnnot=snpAnnot)
  checkIdentical(A, getAlleleA(obj))
  checkIdentical(B, getAlleleB(obj))
  
  gc <- getGenotype(obj, char=TRUE, sort=TRUE)
  checkTrue(all(gc %in% c(NA,"C/C","C/G","G/G")))
  checkIdentical(is.na(geno), is.na(gc))
  checkIdentical(geno == 0, gc == "C/C")
  checkIdentical(geno == 1, gc == "C/G")
  checkIdentical(geno == 2, gc == "G/G")
  
  gc <- getGenotype(obj, char=TRUE, sort=FALSE)
  checkTrue(all(gc %in% c(NA,"C/C","G/C","G/G")))
  checkIdentical(is.na(geno), is.na(gc))
  checkIdentical(geno == 0, gc == "C/C")
  checkIdentical(geno == 1, gc == "G/C")
  checkIdentical(geno == 2, gc == "G/G")

  # check subset of snps and scans
  gc <- getGenotype(obj, snp=c(1,10), scan=c(2,2), char=TRUE)
  checkIdentical(is.na(geno[1:10,2:3]), is.na(gc))
  checkIdentical(geno[1:10,2:3] == 0, gc == "C/C")
  checkIdentical(geno[1:10,2:3] == 1, gc == "C/G")
  checkIdentical(geno[1:10,2:3] == 2, gc == "G/G")
}

test_GenotypeData_selection <- function() {
  file <- tempfile()
  gds <- createfn.gds(file)
  snp <- 1:260
  chrom <- rep(1:26, each=10)
  pos <- rep(1001:1026, 10)
  samp <- 1231:1235
  nsnp <- length(snp)
  nsamp <- length(samp)
  geno <- matrix(sample(0:3, nsnp*nsamp, replace=TRUE),
                 nrow=nsnp, ncol=nsamp)
  add.gdsn(gds, "snp.id", snp)
  add.gdsn(gds, "snp.chromosome", chrom)
  add.gdsn(gds, "snp.position", pos)
  add.gdsn(gds, "sample.id", samp)
  add.gdsn(gds, "genotype", geno, storage="bit2")
  closefn.gds(gds)

  snpAnnot <- SnpAnnotationDataFrame(data.frame(snpID=snp, chromosome=chrom, position=pos, alleleA="C", alleleB="G"))
  gdsobj <- GdsGenotypeReader(file)
  obj <- GenotypeData(gdsobj, snpAnnot=snpAnnot)
  geno[geno == 3] <- NA
  checkIdentical(geno[1:10,1:2], getGenotypeSelection(obj, snp=1:10, scan=1:2, use.names=FALSE))
  checkIdentical(geno[1:10,1:2], getGenotypeSelection(obj, snpID=1:10, scanID=1231:1232, use.names=FALSE))
  geno[geno %in% 0] <- "G/G"
  geno[geno %in% 1] <- "C/G"
  geno[geno %in% 2] <- "C/C"
  checkIdentical(geno[1:10,1:2], getGenotypeSelection(obj, snp=1:10, scan=1:2, char=TRUE, use.names=FALSE))
  checkIdentical(geno[1:10,1:2], getGenotypeSelection(obj, snpID=1:10, scanID=1231:1232, char=TRUE, use.names=FALSE))

  close(obj)
  unlink(file)
}