getResult-methods: Returns the 'result' parameter

Description Usage Arguments Value Author(s) See Also Examples

Description

Returns the result parameter stored in the specified object. If the object is of class DEMIExperiment then it returns a list of DEMIResult objects. If the object is of class DEMIDiff then it returns only one DEMIResult object. But if the object is of class DEMIResult then the function returns a list that contains the results for every cluster in a data.frame. However instead of using this function it maybe easier to use the function getResultTable that returns the result parameter as a data.frame.

Usage

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getResult(object)

## S4 method for signature 'DEMIDiff'
getResult(object)

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

## S4 method for signature 'DEMIResult'
getResult(object)

Arguments

object

A DEMIExperiment, DEMIDiff or DEMIResult object.

Value

Returns the result parameter. For objects of class DEMIExperiment it returns a list of DEMIResult objects. For objects of class DEMIDiff it returns a single DEMIResult object and for objects of class DEMIResult it returns a list.

Author(s)

Sten Ilmjarv

See Also

DEMIExperiment, DEMIDiff, DEMIResult, getResultTable

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 getResult

# Set up an experiment
demiexp <- DEMIExperiment( analysis = 'gene', celpath = destfolder,
			experiment = 'myexperiment', organism = 'homo_sapiens' )

# Create clusters with an optimized wilcoxon's rank sum test incorporated within demi that
# precalculates the probabilities
demiclust <- DEMIClust( demiexp, group = c( "BRAIN", "UHR" ), clust.method = demi.wilcox.test.fast )

# Calcuate differential expression
demidiff <- DEMIDiff( demiclust )

# Attach results from 'DEMIDiff' object to 'DEMIExperiment' object
demiexp_attached <- attachResult( demiexp, demidiff )

# Retrieve the 'result' parameter
getResult( demiexp_attached )
getResult( demidiff )


## End(Not run)

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