check4probe-methods: Checks if the probes are available

In demi: Differential Expression from Multiple Indicators

Description

The function check4probe checks if the probe ID's specified in the probes vector are present in the alignment data of the specified DEMIExperiment object.

Usage

check4probe(object, probes)

## S4 method for signature 'DEMIExperiment,vector'
check4probe(object, probes)

Arguments

object	A DEMIExperiment object.
probes	A vector. A vector of probe ID's.

Details

To see which probes are available in the alignment data use the function getAlignment(x)$probeID where x is an object of class DEMIExperiment.

Value

Returns NULL if all the probes are exist in the alignment data, else returns an error message.

Author(s)

Sten Ilmjarv

See Also

DEMIExperiment

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 check4probe

# 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 )

# Check for probe ID's
check4probe( demiexp, c( 1155955, 100210 ) )

# To see what probes gave the error
setdiff( c( 1155955, 100210 ), getAlignment( demiexp )$probeID )


## End(Not run)

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