inst/doc/largeData.R

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

## ----message = FALSE----------------------------------------------------------
library(sesame)
options(rmarkdown.html_vignette.check_title = FALSE)

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fset <- openSesameToFile('mybetas',
    system.file('extdata',package='sesameData'))

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fset

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head(fset$samples) # sample IDs
head(fset$probes) # probe IDs

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sliceFileSet(fset, '4207113116_B', c('cg00006414','cg00007981'))

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fset <- readFileSet('mybetas')
sliceFileSet(fset, '4207113116_A', 'cg00000292')

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fset2 <- initFileSet('mybetas2', 'HM450', c('sample1', 'sample2'))

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hypothetical_betas <- setNames(runif(fset2$n), fset2$probes)
mapFileSet(fset2, 'sample2', hypothetical_betas)

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abs(sliceFileSet(fset2,'sample2','cg00000108') -
        hypothetical_betas['cg00000108']) < 1e-7