Description Details Value See Also
The methimputeBinomialHMM
is a list() which contains various entries (see Value section). The main entry of this object is $data
, which contains the methylation status calls and posterior values. See Details for a description of all columns.
The $data
entry in this object contains the following columns:
context The sequence context of the cytosine.
counts Counts for methylated and total number of reads at each position.
distance The distance in base-pairs from the previous to the current cytosine.
transitionContext Transition context in the form "previous-current".
posteriorMax Maximum posterior value of the methylation status call, can be interpreted as the confidence in the call.
posteriorMeth Posterior value of the "methylated" component.
posteriorUnmeth Posterior value of the "unmethylated" component.
status Methylation status.
rc.meth.lvl Recalibrated methylation level, calculated as r$data$rc.meth.lvl = r$data$params$emissionParams$Unmethylated[data$context,] * r$data$posteriorUnmeth + r$params$emissionParams$Methylated[data$context,] * r$data$posteriorMeth
, where r
is the methimputeBinomialHMM
object.
A list() with the following entries:
convergenceInfo |
A list() with information about the convergence of the model fitting procedure. |
params |
A list() with fitted and non-fitted model parameters. |
params.initial |
A list() with initial values for the model parameters. |
data |
A |
segments |
The |
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