produceGEOPlatformFile: Produce GEO Platform Submission File in SOFT format

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

Description

Produce GEO Sample Submission File in SOFT format based on the provided LumiBatch object and Illumina ID Mapping library

Usage

produceGEOPlatformFile(x.lumi, lib.mapping = NULL, nuIDMode = TRUE, includeAllChipProbe=FALSE, fileName = "GEOPlatformFile.txt")

Arguments

x.lumi	The LumiBatch object keeping all probes
lib.mapping	The Illumina ID Mapping library, e.g., "lumiHumanIDMapping"
nuIDMode	Determine whether producing the platform indexed by nuID
includeAllChipProbe	Determine whether including all probes in the Manifest file or just the probes used in the x.lumi object
fileName	Filename of the GEO Platform File name

Details

The function produces the GEO platform submission file based on the chip information kept in the Illumina ID Mapping library (specified by lib.mapping parameter). The determination of chip type will be automatically done by selecting the best matching of the probe IDs with individual chips.

Value

Save the result as a text file in SOFT platform submission format.

Author(s)

Pan Du

References

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

See Also

produceGEOSubmissionFile

Examples

# data(example.lumi)
# produceGEOPlatformFile(example.lumi, lib.mapping='lumiHumanIDMapping')

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