demi (version 1.1.2)

getCutoffPvalue: Returns the cutoff.pvalue parameter

Description

Returns the cutoff.pvalue parameter of the 'DEMIClust' object. It is used to determine the cutoff significance level of probe signalling when applying the clustering function.

Usage

getCutoffPvalue(object)
"getCutoffPvalue"(object)

Arguments

object

A DEMIClust object.

Value

Returns the cutoff.pvalue parameter of the 'DEMIClust' object.

See Also

DEMIClust

Examples

## 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 getCutoffPvalue
# 
# # 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 )
# 
# # Retrieve the 'cutoff.pvalue' parameter
# getCutoffPvalue( demiclust )
# 
# ## End(Not run)