produceGEOSubmissionFile {lumi} | R Documentation |
Produce GEO Sample Submission File in the SOFT format based on the provided LumiBatch object and sample information
produceGEOSubmissionFile(lumiNormalized, lumiRaw, lib.mapping, sampleInfo = NULL, fileName = "GEOSubmissionFile.txt", supplementaryRdata = TRUE)
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" |
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. |
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 suggested 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'.
Save the result as a text file in SOFT sample submission format. The supplementary Rdata will be saved in a file 'supplementaryData.Rdata'.
Pan Du
http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html
produceGEOSampleInfoTemplate
, produceGEOPlatformFile
## 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')