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)