## Not run:
# library(GWASdata)
#
# #############
# # Illumina - genotype file
# #############
# # first create empty netCDF
# data(illumina_snp_annot)
# snpAnnot <- illumina_snp_annot
# data(illumina_scan_annot)
# scanAnnot <- illumina_scan_annot[1:3,] # subset of samples for testing
# ncfile <- tempfile()
# ncdfCreate(snpAnnot, ncfile, variables="genotype",
# n.samples=nrow(scanAnnot))
#
# # add data
# path <- system.file("extdata", "illumina_raw_data", package="GWASdata")
# snpAnnot <- snpAnnot[,c("snpID", "rsID")]
# names(snpAnnot) <- c("snpID", "snpName")
# scanAnnot <- scanAnnot[,c("scanID", "genoRunID", "file")]
# names(scanAnnot) <- c("scanID", "scanName", "file")
# col.nums <- as.integer(c(1,2,12,13))
# names(col.nums) <- c("snp", "sample", "a1", "a2")
# diagfile <- tempfile()
# res <- ncdfAddData(path, ncfile, snpAnnot, scanAnnot, sep.type=",",
# skip.num=11, col.total=21, col.nums=col.nums,
# scan.name.in.file=1, diagnostics.filename=diagfile)
#
# file.remove(diagfile)
# file.remove(ncfile)
#
# #############
# # Affymetrix - genotype file
# #############
# # first create empty netCDF
# data(affy_snp_annot)
# snpAnnot <- affy_snp_annot
# data(affy_scan_annot)
# scanAnnot <- affy_scan_annot[1:3,] # subset of samples for testing
# ncfile <- tempfile()
# ncdfCreate(snpAnnot, ncfile, variables="genotype",
# n.samples=nrow(scanAnnot))
#
# # add data
# path <- system.file("extdata", "affy_raw_data", package="GWASdata")
# snpAnnot <- snpAnnot[,c("snpID", "probeID")]
# names(snpAnnot) <- c("snpID", "snpName")
# scanAnnot <- scanAnnot[,c("scanID", "genoRunID", "chpFile")]
# names(scanAnnot) <- c("scanID", "scanName", "file")
# col.nums <- as.integer(c(2,3)); names(col.nums) <- c("snp", "geno")
# diagfile <- tempfile()
# res <- ncdfAddData(path, ncfile, snpAnnot, scanAnnot, sep.type="\t",
# skip.num=1, col.total=6, col.nums=col.nums,
# scan.name.in.file=-1, diagnostics.filename=diagfile)
# file.remove(diagfile)
#
# # check
# diagfile <- tempfile()
# res <- ncdfCheckGenotype(path, ncfile, snpAnnot, scanAnnot, sep.type="\t",
# skip.num=1, col.total=6, col.nums=col.nums,
# scan.name.in.file=-1, check.scan.index=1:3,
# n.scans.loaded=3, diagnostics.filename=diagfile)
# file.remove(diagfile)
# file.remove(ncfile)
#
# #############
# # Affymetrix - intensity file
# #############
# # first create empty netCDF
# snpAnnot <- affy_snp_annot
# scanAnnot <- affy_scan_annot[1:3,] # subset of samples for testing
# ncfile <- tempfile()
# ncdfCreate(snpAnnot, ncfile, variables=c("quality","X","Y"),
# n.samples=nrow(scanAnnot))
#
# # add sampleID and quality
# path <- system.file("extdata", "affy_raw_data", package="GWASdata")
# snpAnnot <- snpAnnot[,c("snpID", "probeID")]
# names(snpAnnot) <- c("snpID", "snpName")
# scanAnnot1 <- scanAnnot[,c("scanID", "genoRunID", "chpFile")]
# names(scanAnnot1) <- c("scanID", "scanName", "file")
# col.nums <- as.integer(c(2,4)); names(col.nums) <- c("snp", "qs")
# diagfile <- tempfile()
# res <- ncdfAddData(path, ncfile, snpAnnot, scanAnnot1, sep.type="\t",
# skip.num=1, col.total=6, col.nums=col.nums,
# scan.name.in.file=-1, diagnostics.filename=diagfile)
# file.remove(diagfile)
#
# # add intensity
# scanAnnot2 <- scanAnnot[,c("scanID", "genoRunID", "alleleFile")]
# names(scanAnnot2) <- c("scanID", "scanName", "file")
# diagfile <- tempfile()
# res <- ncdfAddIntensity(path, ncfile, snpAnnot, scanAnnot2,
# diagnostics.filename=diagfile)
# file.remove(diagfile)
#
# # check
# intenpath <- system.file("extdata", "affy_raw_data", package="GWASdata")
# scanAnnot <- scanAnnot[,c("scanID", "genoRunID", "chpFile", "alleleFile")]
# names(scanAnnot) <- c("scanID", "scanName", "file", "inten.file")
# diagfile <- tempfile()
# res <- ncdfCheckIntensity(path, intenpath, ncfile, snpAnnot, scanAnnot, sep.type="\t",
# skip.num=1, col.total=6, col.nums=col.nums,
# scan.name.in.file=-1, check.scan.index=1:3,
# n.scans.loaded=3, affy.inten=TRUE,
# diagnostics.filename=diagfile)
#
# file.remove(diagfile)
# file.remove(ncfile)
# ## End(Not run)
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