ping {PING}R Documentation

Estimation of binding site positions

Description

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

Usage

PING(segReadsList, paraEM=NULL, paraPrior=NULL, dataType="MNase", detail=0, rescale=1, nCores=1)

Arguments

segReadsList

This object contains segmentation of Genome

paraEM

A list of parameters for the EM algorithm. The default parameters should be good enough for most usages.

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

maxK: an integer, default=0. 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="AIC3"

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. The default parameters should be good enough for most usages.

xi: an integer, default=150. The average DNA fragment size.

rho: an integer, default=1.2. A variance parameter for the average DNA fragment size distribution.

alpha: an integer, default=10. First hyperparameter of the inverse Gamma distribution for sigma^2 in the PICS model

beta: an integer, default=20000. Second hyperparameter of the inverse Gamma distribution for sigma^2 in the PING model

lambda: an integer, default=0.000064. The precision of the prior for mu used for histone data.

dMu: an integer, default=200. Our best guess for the distance between two neighboring nucleosomes.

dataType

A character string that can be set to use selected default parameters for the algorithm.

detail

An integer. Additional information are printed if set to a value > 0.

rescale

An integer.

nCores

An integer. The number of cores that should be used in parallel by the function.

Methods

code

signature(x = "ping"): return the error code for each list element (i.e. candidate region) of a PING object. If the string is empty, there were no errors.

plot

signature(x = "ping"): Plot all regions in the PING object. This might be long, and should only be used to plot a few regions, so subset the object before plotting.

sigmaSqR

signature(x = "ping"): return the variance parameter of the reverse (R) distribution for each binding event.

sigmaSqF

signature(x = "ping"): return the variance parameter of the forward (F) distribution for each binding event.

score

signature(x = "ping"): return the score for each binding event.

scoreF

signature(x = "ping"): return the score of the forward (F) for each binding event.

scoreR

signature(x = "ping"): return the score of the forward (R) for each binding event.

maxRange

signature(x = "ping"): return the range maximum.

minRange

signature(x = "ping"): return the range minimal.

K

signature(x = "ping"): subset PING object.

density

signature(x = "ping"): return the density for each binding event.

Author(s)

Xuekui Zhang, ubcxzhang@gmail.com and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Sangsoon Woo, swoo@fhcrc.org

See Also

ping


[Package PING version 2.28.0 Index]