getTargetProbes-methods: Returns the probe ID's of the specified targets

In demi: Differential Expression from Multiple Indicators

Description

The function getTargetProbes returns the probe ID's of the specified targets. Depending on the analysis parameter in the underlying DEMIExperiment object the target parameter can be an ensembl gene ID or gene symbol (e.g. 'MAOB'), ensembl transcript ID, ensembl peptide ID or genomic region ID.

Usage

getTargetProbes(object, target)

## S4 method for signature 'DEMIDiff,vector'
getTargetProbes(object, target)

## S4 method for signature 'DEMIExperiment,vector'
getTargetProbes(object, target)

Arguments

object	A DEMIExperiment or DEMIDiff object.
target	A vector. A vector of targets whose probe ID's should be returned. Depending on the analysis the target can be ensembl gene ID or gene symbol (e.g. 'MAOB'), ensembl transcript ID, ensembl peptide ID or genomic region ID.

Details

To see available targets used in the analysis you can try head(getAnnotation(x)) where x is an object of class DEMIExperiment. Alternatively you could use head(getAnnotation(getExperiment(y))) where y is of class DEMIDiff.

Value

Returns the probes ID's specified by the targets.

Author(s)

Sten Ilmjarv

See Also

DEMIExperiment, DEMIDiff

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 getTargetProbes

# 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 )

# Retrieve the probe ID's of the specified targets
getTargetProbes( demiexp, "MAOB" )
getTargetProbes( demidiff, "MAOB" )


## End(Not run)

demi documentation built on May 2, 2019, 11:11 a.m.