PICS (version 2.16.0)

pics: Estimation of binding site positions

Description

This object contains Estimation of binding site positions and has the following slots: segReadsList, dataType.

Usage

PICS(segReadsList,dataType=NULL, paraEM=NULL, paraPrior=NULL, nCores=1)

Arguments

segReadsList
This object contains segmentation of Genome
dataType
The type of data you are processing: specified `TF' for transcription factor.
paraEM
A list of parameters for the EM algorithm as returned by the setParaEm function. The default parameters should be good enough for most usages.
paraPrior
A list of parameters for the prior distribution as returned by the setParaPrior function. The default parameters should be good enough for most usages.
nCores
An integer. The number of cores that should be used in parallel by the function.

Methods

code
signature(x = ``pics''): return the error code for each list element (i.e. candidate region) of a PICS object. If the string is empty, there were no errors.
plot
signature(x = ``pics''): Plot all regions in the PICS object. This might be long, and should only be used to plot a few regions, so subset the object before plotting.
sigmaSqR
signature(x = ``pics''): return the variance parameter of the reverse (R) distribution for each binding event.
sigmaSqF
signature(x = ``pics''): return the variance parameter of the forward (F) distribution for each binding event.
score
signature(x = ``pics''): return the score for each binding event.
scoreF
signature(x = ``pics''): return the score of the forward (F) for each binding event.
scoreR
signature(x = ``pics''): return the score of the forward (R) for each binding event.
maxRange
signature(x = ``pics''): return the range maximum.
minRange
signature(x = ``pics''): return the range minimal.
K
signature(x = ``pics''): subset PICS object.
wigDensity
signature(x = ``pics''): return the density for each binding event.

References

X. Zhang, G. Robertson, M. Krzywinski, K. Ning, A. Droit, S. Jones, and R. Gottardo, ``PICS: Probabilistic Inference for ChIP-seq'' arXiv, 0903.3206, 2009. To appear in Biometrics.

See Also

pics