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

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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

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## 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')

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