getCytoband-methods: Returns the 'cytoband' parameter representing karyotype...

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

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getCytoband(object)

## S4 method for signature 'DEMIExperiment'
getCytoband(object)

Arguments

object

A DEMIExperiment object.

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.

Value

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

Author(s)

Sten Ilmjarv

See Also

DEMIExperiment

Examples

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## 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)

demi documentation built on May 30, 2017, 2:40 a.m.