canopy.cluster.Estep: E-step of EM algorithm for multivariate clustering of SNAs

Description Usage Arguments Value Author(s) Examples

View source: R/canopy.cluster.Estep.R

Description

E-step of EM algorithm for multivariate clustering of SNAs. Used in canopy.cluster.

Usage

1
    canopy.cluster.Estep(Tau, Mu, R, X)

Arguments

Tau

prior for proportions of mutation clusters

Mu

MAF centroid for each mutation cluster in each sample

R

alternative allele read depth matrix

X

total read depth matrix

Value

Matrix of posterior probability of cluster assignment for each mutation.

Author(s)

Yuchao Jiang [email protected]

Examples

1
2
3
4
5
6
    data(AML43)
    R = AML43$R
    X = AML43$X
    Mu = AML43$Mu
    Tau = AML43$Tau
    pG = canopy.cluster.Estep(Tau, Mu, R, X)

Example output

Loading required package: ape
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps
Loading required package: pheatmap
Loading required package: scatterplot3d

Canopy documentation built on Dec. 23, 2017, 5:09 p.m.