inst/testScripts/system/chipTypes/Hs_PromPR_v02/31.AromaCellCpgFile.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

###########################################################################/**
# File type test
#
# Description:
# This test verifies that aroma.affymetrix can create AromaCellCpgFile
# and AromaCellPositionFile objects for the (promoter) tiling array.
#
# Author: Mark Robinson
# Created: 2010-02-22
# Last modified: 2012-09-02
#*/###########################################################################
library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup the chip type
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType("Hs_PromPR_v02")
print(cdf)

cdfU <- getUniqueCdf(cdf)
print(cdfU)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Test allocation, writing and reading of 'acp' object
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allocate
acp <- AromaCellPositionFile$allocateFromCdf(cdfU, tags=c("*", "test"), 
                                            overwrite=TRUE, verbose=verbose)
print(acp)

nbrOfRandomCells <- 20
cells <- sample(nbrOfCells(cdfU), size=nbrOfRandomCells)
chr <- sample(1:22, size=nbrOfRandomCells)
pos <- sample(1:1e6, size=nbrOfRandomCells)

# Write
acp[cells,1] <- chr
acp[cells,2] <- pos

# Read
cp <- acp[cells,]

# Sanity check
stopifnot((cp[,1] == chr) & (cp[,2] == pos))

# Clean up
rm(chr, pos, cp)
file.remove(getPathname(acp))

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Test allocation, writing and reading of 'acc' object
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allocate
acc <- AromaCellCpgFile$allocateFromCdf(cdfU, tags=c("*", "test"), 
                                            overwrite=TRUE, verbose=verbose)
print(acc)

cells <- sample(nbrOfCells(cdfU), size=nbrOfRandomCells)
cpg <- rnorm(nbrOfRandomCells)

# Write
acc[cells,1] <- 2^cpg

# Read
cpg2 <- acc[cells,1,drop=TRUE]

d <- (log2(cpg2) - cpg)^2
print(summary(d))

# Sanity check
stopifnot(sum(d) < 1e-8)

# Clean up
file.remove(getPathname(acc))