getPathway: Returns the `pathway` parameter representing functional annotation information

Description

Returns the pathway parameter of the DEMIExperiment object. It is a data.frame that stores information about gene ontology categories.

Usage

getPathway(object)
"getPathway"(object)

Arguments

object

A DEMIExperiment object.

Value

Returns the pathway parameter of the DEMIExperiment object that is a data.frame.

Details

The information about gene ontology categories is used when the user runs pathway analysis on DEMI differential expression results with the function DEMIPathway.

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 getPathway. Note that pathway can only
# # be retrieved if the analysis is set to gene or transcript.
# 
# # Set up an experiment
# demiexp <- DEMIExperiment( analysis = 'gene', celpath = destfolder,
# 			experiment = 'myexperiment', organism = 'homo_sapiens' )
# 
# # Retrieve the 'pathway' parameter representing functional annotation information
# head( getPathway( demiexp ) )
# 
# ## End(Not run)