Simulator-class: Virtual class containing general methods for simulators based...

In Neurergus/MOSim: Multi-Omics Simulation (MOSim)

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.

Neurergus/MOSim documentation built on Feb. 23, 2024, 8:29 a.m.