MOSimulatorRegion-class {MOSim} | R Documentation

## Virtual class containing general methods for simulators based on regions of the chromosomes, like DNase-seq, ChIP-seq or Methyl-seq

### Description

Virtual class containing general methods for simulators based on regions of the chromosomes, like DNase-seq, ChIP-seq or Methyl-seq

Class to simulate RNA-seq data

Class to simulate transcription factor data

Class to simulate miRNA-seq

Class to simulate ChIP-seq data

Class to simulate DNase-seq data

Class to simulate Methyl-seq data.

### Slots

`locs`

  Vector containing the list of locations of the sites.

`locsName`

  Type of the site to simulate, only for debug.

`splitChar`

  Character symbol used to split identifiers in chr/start/end

`nCpG`

  numeric. Number of CpG sites to simulate.

`pSuccessMethReg`

  numeric. Probability of success in methylated region.

`pSuccessDemethReg`

  numeric. Probability of success in non methylated region

`errorMethReg`

  numeric. Error rate in methylated region

`errorDemethReg`

  numeric. Error rate in methylated region

`nReadsMethReg`

  numeric. Mean number of reads in methylated region.

`nReadsDemethReg`

  numeric. Mean number of reads in non methylated regions.

`phaseDiff`

  numeric. Phase difference in the differentially methylated regions between two samples

`balanceHypoHyper`

  numeric. Balance of hypo/hyper methylation

`ratesHMMMatrix`

  numeric. Matrix of values that describes the exponential decay functions that define the distances between CpG values.

`distType`

  character. Distribution used to generate replicates:

`transitionSize`

  numeric.

`PhiMeth`

  matrix. Transition matrix for CpG locations.

`PhiDemeth`

  matrix. <Not used>

`typesLocation`

  numeric. <Not used>

`returnValue`

  character. Selected column:

`betaThreshold`

  numeric. Beta threshold value used to calculate M values.

[Package MOSim version 1.8.0 Index]