agilp (version 3.8.0)

IDswop: Mapping expression data across bioinformatic identifiers

Description

This script maps expression data associated with a source identifier (typically a platform specific identifier such as ProbeID, as output by AAProcess in the agilp package for example), to another identifier of the user's choice. The script uses an annotation file which contains the mappings between identifiers. Each column denotes a different identifier, which is shown in the column heading. Typical examples include ProbeID, EntrezGeneID, EnsemblTranscriptID etc.) Annotation files are provided by microarray manufacturers,or, preferably are created using, for example the biomaRt package in Bioconductor.

Usage

IDswop(input=file.path(system.file(package="agilp"),"input",""),output=file.path(system.file(package="agilp"),"output",""),fun="mean",annotation=file.path(system.file(package="agilp"),"input1","annotation.txt"), source_ID = "ProbeID", target_ID="EnsemblID", ERR=0.2)

Arguments

input

full path of directory where input data files are put; default is a folder named input within the agilp package directory; the input directory must contain ONLY the set of files to be processed. The input files must contain two columns only, the source identifier in the first column, and the expression data in the second column; see example files in datasets folder

output

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

fun

the function to be applied in cases where multiple probes map to the same identifier; currently allowed values are "mean" or "max".

annotation

full path of annotation file; default is a file called annotation.txt within a folder named input1 within the agilp package directory

source_ID

The identifier from which the data is mapped. This must appear exactly as it appears in the heading of the appropriate column of the annotation file.

target_ID

The identifier to which the data is mapped. This must appear exactly as it appears in the heading of the appropriate column of the annotation file

ERR

The cut-off for coefficient of variation allowed when multiple probes map to a single identifier. ERR must lie between 0 and 1. If ERR=0, any difference between such probes will result in the identifier being omitted from the final list. If ERR=1, all identifiers are retained. The default is 0.2, allowing a maximum coefficient of variation between multiple probes mapping to a single identifier of 20%.

Value

remapped datafiles

One new file is produced for each input file. Each file contains two columns; the first contains the new set of identifiers; the second contains the corresponding expression value. The file name contains the new identifier as a suffix.

Details

This function is designed for merging expression data sets from different platforms using common bioinformatic identifiers such as gene names, transcript names etc. The major problem lies in how to deal with the "many to many" mapping which characterise the relationships between most standard identifiers. IDswop deals with the problem as follows. If multiple source identifiers (typically platform specific probe IDs) map to a single target (for example Ensembl_Transcript_ID ) , the different probes are either averaged (fun="mean") or the maximum is selected (fun="max"). However, in cases where the discrepancy between such sets of probes is too large, the identifier is discarded, since it is considered as being unreliable. The degree of error allowed can be set by the user, as described under a descrition of the ERR variable given above. In cases where a single source identifier maps to multple targets (e.g. one probe to several transcript IDs) each transcript is retained as a separate entry in the final list, with an identical expression value.

References

In preparation

See Also

AAProcess filenamex Loader Baseline Equaliser AALoess

Examples

#This examples maps expression data from Agilent ProbeIDs (found in column one of input files) to corresponding EnsemblID. Each output file has the name of the original file with the suffix "_EnsemblID". If multiple probes map to teh same ID and vary by more than 20% they are discarded.


inputdir<-file.path(system.file(package="agilp"),"extdata","raw","", fsep = .Platform$file.sep)
outputdir<-file.path(system.file(package="agilp"),"output", "", fsep = .Platform$file.sep)
annotation<-file.path(system.file(package="agilp"),"extdata","annotations_sample.txt", fsep = .Platform$file.sep)
IDswop(input=inputdir,output=outputdir,annotation=annotation,source_ID="ProbeID",target_ID="EnsemblID", ERR=0.2)

#Alternatively the following keeps all output IDs, even when multiple probes map to a single

IDswop(input=inputdir,output=outputdir,annotation=annotation,source_ID="ProbeID",target_ID="EnsemblID", ERR=1)

## 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)