ping {PING} | R Documentation |
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. |
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 |
rescale |
An |
nCores |
An |
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.
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.
signature(x = "ping")
: return the variance parameter of the reverse (R) distribution for each binding event.
signature(x = "ping")
: return the variance parameter of the forward (F) distribution for each binding event.
signature(x = "ping")
: return the score for each binding event.
signature(x = "ping")
: return the score of the forward (F) for each binding event.
signature(x = "ping")
: return the score of the forward (R) for each binding event.
signature(x = "ping")
: return the range maximum.
signature(x = "ping")
: return the range minimal.
signature(x = "ping")
: subset PING object.
signature(x = "ping")
: return the density for each binding event.
Xuekui Zhang, ubcxzhang@gmail.com and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Sangsoon Woo, swoo@fhcrc.org