aroma.affymetrix (version 2.2.0)

getGenomeInformation.AffymetrixCdfFile: Gets genome information for this chip type

Description

Gets genome information for this chip type.

Usage

## S3 method for class 'AffymetrixCdfFile':
getGenomeInformation(this, types=c("UGP", "dChip"), ..., force=FALSE, verbose=FALSE)

Arguments

types

A character vector specifying what type of genome information sets to search for.

...

Not used.

force

If FALSE, cached information is retrieved, otherwise not.

verbose

A logical or Verbose.

Value

• Returns a GenomeInformation object.

See Also

For more information see AffymetrixCdfFile.

Examples

for (zzz in 0) {

# Define a CDF for a SNP chip
if (!exists("cdf")) {
  cdf <- AffymetrixCdfFile$fromChipType(".*Sty.*")
}
print(cdf)

# Get the genome information
gi <- getGenomeInformation(cdf)
print(gi)

# Get the units on chromosome X order position by default
# (First call will be slow be data is being cached)
units <- getUnitIndices(gi, chromosome="X")
nunits <- length(units)
cat(sprintf("Number of units on chromosome X: %d\n", nunits))
str(units)

# Plot the SNP density for this chromosome
plotDensity(gi, chromosome="X");

} # for (zzz in 0)
rm(zzz)