We have recently conducted 1.1 million snp/cnv genotyping on a sample of subjects using the infinium assay. The data is currently a project within Illumina GenomeStudio. I have imported some columns containing pedigree, affected status, race and ethnicity to the project but I also have that data in a separate table.
How do I read the data from genomestudio into R? Are you aware of any published examples or case vignettes?
Is beadarraySNP the package to use?
The data seems to be stored in a directory with the following files.
tabledat.bin, pairtable.bin, seqdata.bin, sd.bin, heredity.bin, Duplicates.bin, projdat.bin, PairedData.bin, ad.bin, ld.bin
How does one go from those files to reading the data into R?
I want to end up with a dataframe that has as many rows as I have subjects and as many columns as I have snp markers + cnv markers + pedigree fields + phenotype fields