getGenomeInformation.AffymetrixCdfFile: Gets genome information for this chip type

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

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

## Not run: 
 
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)


## End(Not run)

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.