CNclusterNcenter: TODO

In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events

TODO

Description

TODO

Usage

CNclusterNcenter(
  segrat,
  blsize,
  minJoin,
  nTrial,
  bestBIC,
  modelNames,
  cweight,
  bstimes,
  chromRange
)

Arguments

segrat	a list containing information for one specific profile: seg a data.frame with 3 columns: StartProbe a numeric that tabulates the (integer) start position of each segment in internal units such as probe numbers. EndProbe a numeric that tabulates the (integer) end position of each segment in internal units such as probe numbers. chrom a numeric representing the chromosome. rat a numeric vector of elements that are functions of copy number, most often log ratios of copy number to the expected standard value, such as 2 in diploid genomes for a specific profile. stream a character string representing the profile ID. sub a numeric representing the position of the current profile ID in a vector of profiles.
blsize	a single integer specifying the bootstrap sampling rate of segment medians to generate input for model-based clustering. The number of times a segment is sampled is then given by the (integer) division of the segment length in internal units by blsize.
minJoin	a single numeric value between 0 and 1 specifying the degree of overlap above which two clusters will be joined into one.
nTrial	a single integer specifying the number of times a model-based clustering is attempted for each profile in order to achieve the highest Bayesian information criterion (BIC).
bestBIC	a single numeric value for initializing BIC maximization. A large negative value is recommended.
modelNames	a vector of character strings specifying the names of models to be used in model-based clustering (see package mclust for further details).
cweight	a single numeric value between 0 and 1 specifying the minimal share of the central cluster in each profile.
bstimes	a single double value specifying the number of time the median of each segment is sampled in order to predict the cluster assignment for the segment.
chromRange	a integer vector enumerating chromosomes from which segments are to be used for initial model-based clustering.

Value

a matrix with 9 columns:

• untitled a numeric, the median value of the copy number elements forming each segment

• untitled TODO

• mediandev a numeric, the median function of copy number relative to its central value for each segment

• segerr a numeric, the error estimate for the function of copy number for each segment

• centerz a numeric between 0 and 1, the probability that the segment is in the central cluster

• cpb TODO

• maxz TODO

• maxzmean TODO

• maxzsigma TODO

Author(s)

Alexander Krasnitz, Guoli Sun

Examples

# TODO

## Create a list that contain information about the segments and bins 
## related to one 

KrasnitzLab/CNprep documentation built on May 28, 2022, 8:32 p.m.