agilp (version 3.8.0)

Baseline: Constructs a file with the mean of each probe from a set of raw expression array data files

Description

Calculates the mean expression data for each probe or identifier for a set of expression array data sets, for example as produced by AAProcess. Identifiers (e.g. probe names) must lie in the first column of each file. Identifiers not common to all files in set are discarded. The set of files is either all files in input directory or a set of files defined using a template file. Template is typically an Excel spreadsheet saved as a tab delimited txt fiel, with file names as one column. The files to be used must be specified in a contiguous set of rows of the template file.

Usage

Baseline(NORM="LOG",allfiles="TRUE",r=2,A=2,B=3,input=file.path(system.file(package="agilp"),"input",""),baseout=file.path(system.file(package="agilp"),"output","baseline.txt"),t=file.path(system.file(package="agilp"),"input1","template.txt"))

Arguments

input

full path of directory where input data files are put; default is a folder named input within the agilp package directory

t

full name and path of template file; default is the file template.txt in folder agilp/input1

baseout

full name and path of output file with mean expression values; default is the file baseline.txt in folder agilp/output

NORM

if NORM="LOG", the data are log base 2 transformed before the mean is calculated. The default is NORM="LOG"

r

The column of template which contains the file names

A

The first row of template to be used; note a header row is NOT ignored.

B

The last row of template to be used

allfiles

If allfiles is TRUE, the script uses all files in the input directory, and template is ignored; if allfiles=FALSE, the scritp uses files defined by template

Value

baseout

A tab delimited text file, with each identifier and its mean value,is written to the filename and path defined by baseout

Warning

The function checks that files listed in template exist in folder, and outputs a list of all file names not found

Details

This function is typically used as part of the data processing pipeline to calculate an average against which to normalise all data files using AALoessfunction

References

In preparation

See Also

AAProcess filenamex IDswop Loader Equaliser AALoess

Examples

#Takes four files of raw data in folder agilp/extdata/raw, calculates the mean expression value for each probe, and saves as agilp/output/testbase.txt.

inputdir<-file.path(system.file(package="agilp"),"extdata","raw","", fsep = .Platform$file.sep)
outputbase<-file.path(system.file(package="agilp"),"output", "testbase.txt", fsep = .Platform$file.sep)
template<-file.path(system.file(package="agilp"),"extdata","sample_template.txt", fsep = .Platform$file.sep)
Baseline(NORM="LOG",allfiles="TRUE",r=2,A=2,B=3,input=inputdir, baseout=outputbase, t = template)

#Alternatively the following example uses only those data files defined in column 2, rows 2-5 of the template file. In additon, this example does not log transform the data.
Baseline(NORM="FALSE",allfiles="FALSE",r=2,A=2,B=5,input=inputdir, baseout=outputbase, t = template)

## Not run: 
# #to remove the output files again and empty the output directory use 
# unlink(paste(file.path(system.file(package="agilp"),"output",""),"*.*",sep=""), recursive=FALSE)
# ## End(Not run)