ramr.data {ramr} | R Documentation

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

### Description

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(ramr.data, ramr.samples, ramr.method="beta", min.cpgs=5,
                     merge.window=1000, qval.cutoff=1e-3, cores=2)
      plotAMR(ramr.data, ramr.samples, amrs[1])
      plotAMR(ramr.data, ramr.samples, ramr.tp.nonunique[4],
              highlight=c("sample7","sample8","sample9"))

[Package ramr version 1.2.0 Index]