pics {PICS}R Documentation

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.

minK: an integer, default=1. The minimum number of binding events per region. If the value is 0, the minimum number is automatically calculated.

maxK: an integer, default=15. The maximum number of binding events per region. If the value is 0, the maximum number is automatically calculated.

tol: a numeric, default=1e-4. The tolerance for the EM algorithm.

B: an integer, default=100. The maximum number of iterations to be used.

mSelect: a character string specifying the information criteria to be used when selecting the number of binding events. Default="BIC"

mergePeaks: a logical stating whether overlapping binding events should be picked. Default=TRUE

mapCorrect: a logical stating whether mappability profiles should be incorporated in the estimation, i.e: missing reads estimated. Default=TRUE

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.

xi: an integer, default=200. The average DNA fragment size.

rho: an integer, default=1. A variance parameter for the average DNA fragment size distribution.

alpha: an integer, default=20. First hyperparameter of the inverse Gamma distribution for sigma^2 in the PICS model

beta: an integer, default=40000. Second hyperparameter of the inverse Gamma distribution for sigma^2 in the PING model

lambda: an integer, default=0. The precision of the prior for mu used for histone data.

dMu: an integer, default=0. Our best guess for the distance between two neighboring nucleosomes.

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.

Author(s)

Xuekui Zhang, Arnaud Droit <arnaud.droit@crchuq.ualaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>

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


[Package PICS version 2.28.0 Index]