probe.plot-methods: Draws a plot of the normalized expression levels of the...

In demi: Differential Expression from Multiple Indicators

Description

The function probe.plot draws a plot of the normalized expression levels for the specified targets. 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.

Usage

probe.plot(object, target)

## S4 method for signature 'DEMIExperiment,character'
probe.plot(object, target)

Arguments

object	A DEMIExperiment object.
target	A vector. 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.

Value

A ggplot object.

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 probe.plot

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

# Draw probes levels measuring the gene 'MAOB'
pdf( "MAOB_probe_plot.pdf", width=8, height=8 )
probe.plot( demiexp, "MAOB" )
dev.off()


## End(Not run)

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