Add new alignments to the alignment table

Description

The function addCustomTargets adds additional rows to the alignment table. Before adding new alignments the user needs to verify that the format of the rows corresponds to the format of the alignment table. These new alignments will then be incorporated in the analysis.

Usage

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addCustomTargets(object = "DEMIExperiment", blat = "data.frame",
  anno = "data.frame", overwrite = FALSE)

Arguments

object

A DEMIExperiment object. Determines the experiment where the additional alignment information will be added to.

blat

A data.frame. Represents the added alignments of probes to the target sequences.

anno

A data.frame. Represents the added annotation of the target sequences. If the parameter anno has not been defined then custom annotation will be populated with NA.

overwrite

A logical. If FALSE the previous alignment table will be overwritten. By default it is set to FALSE.

Details

The user needs to make sure that the proper fields in the additional alignment information are not missing. To see which fields are required use the function colnames( getAlignment( x ) ) on the DEMIExperiment object. The two fields that are always required are 'probeID' and 'targetID', the others are optional. All the other fields will be generated automatically and set to NA. If the user knows the annotation information for the targets in the alignment table then it is recommended to add that information to the annotation table. To see what are the fields of annotation table use the function colnames( getAnnotation( x ) ) on the DEMIExperiment object. This information will then be seen later in the analysis results. When adding custom annotations the only field that is required is the 'targetID', all other fields are optional however for later use it is better to add some more information about the target like it's description.

Value

Returns the DEMIExperiment object where the additional information has been added to the alignment table.

Author(s)

Sten Ilmjarv

Examples

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## 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

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

# Create a custom annotation for one target ID
anno <- data.frame("RANDOM_ID", "Some kind of description")
colnames(anno) <- c("targetID", "description")

# Create a custom alignment for one target ID
blat <- data.frame(c(616302,1133177), c("RANDOM_ID","RANDOM_ID"))
colnames(blat) <- c("probeID", "targetID")

# Create a custom alignment for one target ID
customexp <- addCustomTargets(demiexp, blat, anno, FALSE)


## End(Not run)

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