produceMethylationGEOSubmissionFile {lumi} | R Documentation

## Produce GEO Sample Submission File of Illumina methylation microarray data in SOFT format

### Description

Produce GEO Sample Submission File in the SOFT format based on the provided MethyLumiM object and sample information

### Usage

    produceMethylationGEOSubmissionFile(methyLumiM, methyLumiM.raw = NULL, lib.mapping = NULL, idType = "Probe", sampleInfo = NULL, fileName = "GEOSubmissionFile.txt", supplementaryRdata = FALSE, ...)

### Arguments

`methyLumiM` | The normalized data in MethyLumiM class
`methyLumiM.raw` | The raw data in MethyLumiM class
`lib.mapping` | Currently not used for Illumina methylation data
`idType` | Currently no other options for Illumina methylation data
`sampleInfo` | The sample information filename or data.frame, which is returned by `produceGEOSampleInfoTemplate`
`fileName` | The file name of GEO Submission file
`supplementaryRdata` | determine whether produce the Rdata supplement data, which include both methyLumiM and methyLumiM.raw R objects.
`...` | other parameters used by function `nuID2IlluminaID`, but not implemented for methylation data

### Details

The function produces the GEO sample submission file including both normalized and raw data information in the SOFT format. The sample information should be provided by the user as a data.frame or Tab separated text file following the format of the template, which can be produced by function `produceGEOSampleInfoTemplate`. Users need to fill in the detailed sample descriptions in the template, especially the Sample\_title, Sample\_description and some protocols. Users are also required to fill in the "Sample\_platform\_id" by checking information of the GEO Illumina platform.

When the parameter "supplementaryRdata" is TRUE, the R objects, methyLumiM, methyLumiM.raw and sampleInfo, will be saved in a file named 'supplementaryData.Rdata'.

### Value

Save the result as a text file in SOFT sample submission format. The supplementary Rdata will be saved in a file 'supplementaryData.Rdata'.

### Author(s)

Pan Du

### References

http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html

### See Also

`produceGEOSampleInfoTemplate`, `produceGEOPlatformFile`

### Examples

    ## Not run
    ## Produce the sample information template
    # produceGEOSampleInfoTemplate(methyLumiM, fileName = "GEOsampleInfo.txt")
    ## After editing the 'GEOsampleInfo.txt' by filling in sample information
    # produceMethylationGEOSubmissionFile(methyLumiM, methyLumiM.raw, sampleInfo='GEOsampleInfo.txt')

[Package lumi version 2.38.0 Index]