Description Usage Arguments Value Author(s) See Also Examples
Performs wilcox.test
on normalized expression value matrix defined in DEMIClust
object.
1 | demi.wilcox.test(x = "DEMIClust")
|
x |
A |
A list
. Returns a list
containing different sets of probes that behave
similarly under current statistical test (e.g. up- or down-regulated probes).
Sten Ilmjarv
wilcox.test
which this function wraps.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | ## 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 demi.wilcox.test
# Basic experiment set up
demiexp <- DEMIExperiment(analysis = 'gene', celpath = destfolder,
experiment = 'myexperiment', organism = 'homo_sapiens')
# Create clusters with default behaviour
demiclust <- DEMIClust( demiexp, group = c( "BRAIN", "UHR" ) )
# Retrieve probes whose differential signalling was statistically significant
sigprobes <- demi.wilcox.test( demiclust )
# However it makes more sense to incorporate the method straight into \code{DEMIClust} object
demiclust <- DEMIClust( demiexp, group = c( "BRAIN", "UHR" ), clust.method = demi.wilcox.test )
# Retrieve the probes whose differential signalling was statistically significant
sigprobes <- getCluster( demiclust )
# Retrieve the cluster names since we have both up-regulated and down-regulated probe clusters
names( sigprobes )
# Retrieve the up-regulated probes whose cluster names contain the sign '[H]'
head( sigprobes[[grep("\\[H\\]", names( sigprobes ))]] )
# Retrieve the down-regulated probes whose cluster names contain the sign '[L]'
head( sigprobes[[grep("\\[L\\]", names( sigprobes ))]] )
## End(Not run)
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