getPathway-methods: Returns the 'pathway' parameter representing functional...

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

Description

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

Usage

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getPathway(object)

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

Arguments

object

A DEMIExperiment object.

Details

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

Value

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

Author(s)

Sten Ilmjarv

See Also

DEMIExperiment, DEMIPathway

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 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)

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