| getGenomeInformation.AffymetrixCdfFile {aroma.affymetrix} | R Documentation |
Gets genome information for this chip type.
## S3 method for class 'AffymetrixCdfFile':
getGenomeInformation(this, types=c("UGP", "dChip"), ..., force=FALSE, verbose=FALSE)
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. |
Returns a GenomeInformation object.
Henrik Bengtsson (http://www.braju.com/R/)
For more information see AffymetrixCdfFile.
## 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)