produceGEOSubmissionFile: Produce GEO Sample Submission File in SOFT format

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

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

Usage

produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib.mapping = NULL, idType = 'Probe', sampleInfo = NULL, fileName = "GEOSubmissionFile.txt", supplementaryRdata = TRUE, ...)

Arguments

lumiNormalized	The normalized data (LumiBatch object)
lumiRaw	The raw data (LumiBatch object), e.g., returned by lumiR
lib.mapping	The Illumina ID Mapping library, e.g., "lumiHumanIDMapping"
idType	the idType parameter of function nuID2IlluminaID
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 lumiNormalized and lumiRaw R objects.
...	other parameters used by function nuID2IlluminaID

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, lumiNormalized, lumiRaw 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(lumiNormalized, lib.mapping = NULL, fileName = "GEOsampleInfo.txt")
## After editing the 'GEOsampleInfo.txt' by filling in sample information
# produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib='lumiHumanIDMapping', sampleInfo='GEOsampleInfo.txt')

lumi documentation built on Nov. 8, 2020, 5:27 p.m.