pics {PICS} | R Documentation |
This object contains Estimation of binding site positions and has the following slots: segReadsList, dataType.
PICS(segReadsList,dataType=NULL, paraEM=NULL, paraPrior=NULL, nCores=1)
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 |
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 |
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 |
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.
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.
signature(x = ``pics'')
: return the variance parameter of the reverse (R) distribution for each binding event.
signature(x = ``pics'')
: return the variance parameter of the forward (F) distribution for each binding event.
signature(x = ``pics'')
: return the score for each binding event.
signature(x = ``pics'')
: return the score of the forward (F) for each binding event.
signature(x = ``pics'')
: return the score of the forward (R) for each binding event.
signature(x = ``pics'')
: return the range maximum.
signature(x = ``pics'')
: return the range minimal.
signature(x = ``pics'')
: subset PICS object.
signature(x = ``pics'')
: return the density for each binding event.
Xuekui Zhang, Arnaud Droit <arnaud.droit@crchuq.ualaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>
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.