ping: Estimation of binding site positions

Description

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

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

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.

paraPrior

A list of parameters for the prior distribution. The default parameters should be good enough for most usages.

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.

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.