dataSimExample: A 'list' containing methylation information used by some...
In methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description Usage Format Value See Also Examples

A list containing methylation information used by some internal functions (for demo purpose.

1	data(dataSimExample)

a list containing:

stateInfo a GRanges, a synthetic chromosome as generated by getSyntheticChr function.
stateDiff a list containing:
- stateDiff a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using 1, the positions where the CpG sites are differentially methylated.
- stateInherite a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using 1, the positions where the CpG values are inherited.
treatment a vector of integer (0 and 1) with length corresponding the number of samples. The vector indicates which samples are control (0) which samples are case (1).
sample.id a list of 3 list. Each entry of the list correspond to one generation (first entry = first generation, etc..). Each list contains a list of 12 entries each containing a string of character, the name of the sample.

a list containing:

stateInfo a GRanges, a synthetic chromosome as generated by getSyntheticChr function.
stateDiff a list containing:
- stateDiff a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using 1, the positions where the CpG sites are differentially methylated.
- stateInherite a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using 1, the positions where the CpG values are inherited.
treatment a vector of integer (0 and 1) with length corresponding the number of samples. The vector indicates which samples are control (0) which samples are case (1).
sample.id a list of 3 list. Each entry of the list correspond to one generation (first entry = first generation, etc..). Each list contains a list of 12 entries each containing a string of character, the name of the sample.

runSim for running a simulation analysis using methylKit info as input

## Loading dataset
data(dataSimExample)

## Identify differentially methylated sites and among those, the ones
## that are inherited
methInheritSim:::getDiffMeth(stateInfo = dataSimExample$stateInfo, 
    rateDiff = 0.2, minRate = 0.3,propInherite = 0.3)