Simulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples

Data was simulated using GSE51032 data set as described in the reference. Current data set ("ramr.data") contains beta values for 10000 CpGs and 100 samples ("ramr.samples"), and carries 6 unique ("ramr.tp.unique") and 15 non-unique ("ramr.tp.nonunique") true positive AMRs containing at least 10 CpGs with their beta values increased/decreased by 0.5.

Usage

data(ramr)

Format

Objects of class "GRanges" ("ramr.data, ramr.tp.unique, ramr.tp.nonunique") and "character" ("ramr.samples").

References

Nikolaienko et al., 2020 (bioRxiv)

Examples

  data(ramr)
  amrs <- getAMR(
    data.ranges=ramr.data, compute="IQR",
    combine.min.cpgs=5, combine.window=1000, combine.threshold=5
  )
#> Preprocessing data 
#> [0.054s]
#> Computing IQR 
#> [0.003s]
#> Creating genomic ranges 
#> [0.015s]
  plotAMR(data.ranges=ramr.data, amr.ranges=amrs[1])
#> Plotting 1 genomic ranges 
#> 100%
#> [0.135s]
#> $`chr1:2443577-2453006`

#> 
  plotAMR(data.ranges=ramr.data, amr.ranges=ramr.tp.nonunique[4],
          highlight=c("sample7","sample8","sample9"))
#> Plotting 1 genomic ranges 
#> 100%
#> [0.102s]
#> $`chr1:2119531-2122601`

#>