getCytoband: Returns the `cytoband` parameter representing karyotype information

Description

Returns the cytoband parameter of the DEMIExperiment object. It is a data.frame that stores the karyotype information of the chromosomes.

Usage

getCytoband(object)
"getCytoband"(object)

Arguments

object

A DEMIExperiment object.

Value

Returns the cytoband paramter of the DEMIExperiment object that is a data.frame.

Details

If the analysis parameter in DEMIExperiment object is set to 'genome' then genome sections are being annotated by their karyotypes. The annotation information is stored in the cytoband parameter of the DEMIExperiment object.

Examples

Run this code

## Not run: 
# 
# # To use the example we need to download a subset of CEL files from
# # http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9819 published
# # by Pradervand et al. 2008.
# 
# # Set the destination folder where the downloaded files fill be located.
# # It can be any folder of your choosing.
# destfolder <- "demitest/testdata/"
# 
# # Download packed CEL files and change the names according to the feature
# # they represent (for example to include UHR or BRAIN in them to denote the
# # features).
# # It is good practice to name the files according to their features which
# # allows easier identification of the files later.
# 
# ftpaddress <- "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn"
# download.file( paste( ftpaddress, "GSM247694/suppl/GSM247694.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "UHR01_GSM247694.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247695/suppl/GSM247695.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "UHR02_GSM247695.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247698/suppl/GSM247698.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "UHR03_GSM247698.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247699/suppl/GSM247699.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "UHR04_GSM247699.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247696/suppl/GSM247696.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "BRAIN01_GSM247696.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247697/suppl/GSM247697.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "BRAIN02_GSM247697.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247700/suppl/GSM247700.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "BRAIN03_GSM247700.CEL.gz", sep = "" ) )
# download.file( paste( ftpaddress, "GSM247701/suppl/GSM247701.CEL.gz", sep = "/" ),
# 		destfile = paste( destfolder, "BRAIN04_GSM247701.CEL.gz", sep = "" ) )
# 
# # We need the gunzip function (located in the R.utils package) to unpack the gz files.
# # Also we will remove the original unpacked files for we won't need them.
# library( R.utils )
# for( i in list.files( destfolder ) ) {
# 	gunzip( paste( destfolder, i, sep = "" ), remove = TRUE )
# }
# 
# # Now we can continue the example of the function getCytoband
# 
# # Set up an experiment. Note that the cytoband can only retrieved when the analysis
# # has been set to genome.
# demiexp_genome <- DEMIExperiment( analysis = 'genome', celpath = destfolder,
# 		experiment = 'myexperiment', organism = 'homo_sapiens', sectionsize = 500000 )
# 
# # Retrieve the 'cytoband' parameter representing karyotype information
# head( getCytoband( demiexp_genome ) )
# 
# ## End(Not run)