Type: Package
Title: Multiple Change Point
Version: 0.6.3
Maintainer: Brault Vincent <vincent.brault@univ-grenoble-alpes.fr>
Description: Nonparametric approach to estimate the location of block boundaries (change-points) of non-overlapping blocks in a random symmetric matrix which consists of random variables whose distribution changes from block to block. BRAULT Vincent, OUADAH Sarah, SANSONNET Laure and LEVY-LEDUC Celine (2017) <doi:10.1016/j.jmva.2017.12.005>.
Imports: Matrix, capushe, shiny, utils, methods, Rcpp
Collate: MuChPoint_Class.R RcppExports.R MuChPoint.R
URL: https://github.com/Lionning/MuChPoint
BugReports: https://github.com/Lionning/MuChPoint/issues
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.1.2
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-04-08 14:09:43 UTC; Vincent
Author: Brault Vincent [cre, aut], Cougoulat Glenn [ctb], Ouadah Sarah [ctb], Sansonnet Laure [ctb]
Repository: CRAN
Date/Publication: 2022-04-08 14:22:31 UTC

Compute the Delta of the dynamic programming

Description

Compute the Delta of the dynamic programming in Rcpp

Usage

Compute_Cn1n2(x)

Arguments

x

the matrix of rank

MuChPoint fitting procedure

Description

Produce a block-wise estimation of a symmetric matrix.

Usage

MuChPoint(Y, Lmax = nrow(Y)/2, N = NULL, cores = 1, verbose = TRUE)

Arguments

Y

symmetric matrix of observations.

Lmax

a positive integer less than number of columns (and number of rows). By default, nrow(Y)/2.

N

a positive integer vector less than number of columns (and number of rows). N is used when the break-points are known. By default, NULL.

cores

a positive integer giving the number of cores used. If you use windows, the parallelization is impossible. By default, 1.

verbose

logical. To display the progression bars. By default TRUE.

References

Article: BRAULT V., OUADAH S., SANSONNET L. and LEVY-LEDUC C. Nonparametric homogeneity tests and multiple change-point estimation for analyzing large Hi-C data matrices. Journal of Multivariate Analysis, 2017

Examples

require(MuChPoint)
mu=c(rep(c(rep(1,25),rep(0,25)),3))%*%t(rep(c(rep(0,25),rep(1,25)),3))
Y=matrix(rnorm(150^2,0,5),150)+mu+t(mu)
Y=as.matrix(Matrix::forceSymmetric(Y))
res=MuChPoint(Y)
plot(res,Y,L=5,shiny=FALSE)
plot(res,Y,L=1:10,shiny=FALSE,ask=FALSE)

Class "MuChPoint"

Description

Class of object returned by the MuChPoint function.

Usage

## S4 method for signature 'MuChPoint'
show(object)

Arguments

object

an object with class MuChPoint

Slots

S

a vector object of type numeric, giving the values of the statistics S_n(n_1,...,n_L) following the number L.

N

a numeric vector with the position of the different break-points.

bt

an inferior triangular matrix containing the positions of break-points following the number of break-points (in rows).

References

Article: BRAULT V., OUADAH S., SANSONNET L. and LEVY-LEDUC C. Nonparametric homogeneity tests and multiple change-point estimation for analyzing large Hi-C data matrices. Journal of Multivariate Analysis, 2017

See Also

See also plot,MuChPoint-method and MuChPoint.

Produce a plot of two-dimensional segmentation of a MuChPoint fit.

Description

Produce a plot of two-dimensional segmentation of a MuChPoint fit.

Usage

## S4 method for signature 'MuChPoint'
plot(x, y, shiny = TRUE, col = "Color", L = NULL, ask = TRUE)

Arguments

x

an object of class MuChPoint.

y

used for S4 compatibility represented the matrix (typically, the matrix used in the program MuChPoint).

shiny

for a representation with a shiny application.

col

for the colors of the representations.

L

the summarized matrix with L break-points (L can be a vector).

ask

If TRUE, to hit will be necessary to see next plot.

References

Article: BRAULT V., OUADAH S., SANSONNET L. and LEVY-LEDUC C. Nonparametric homogeneity tests and multiple change-point estimation for analyzing large Hi-C data matrices. Journal of Multivariate Analysis, 2017

See Also

MuChPoint, capushe.

Examples

require(MuChPoint)
mu=c(rep(c(rep(1,25),rep(0,25)),3))%*%t(rep(c(rep(0,25),rep(1,25)),3))
Y=matrix(rnorm(150^2,0,2),150)+mu+t(mu)
Y=as.matrix(Matrix::forceSymmetric(Y))
res=MuChPoint(Y)
plot(res,Y,L=5,shiny=FALSE)
plot(res,Y,L=1:10,shiny=FALSE,ask=FALSE)

Print for the class of object returned by the MuChPoint function.

Description

Print for the class of object returned by the MuChPoint function.

Usage

## S4 method for signature 'MuChPoint'
print(x, N = NULL)

Arguments

x

an object with class MuChPoint

N

a numeric between 1 and length(x@N) for the number of break-points desired.

Summary of a MuChPoint object.

Description

Summary of a MuChPoint object.

Usage

## S4 method for signature 'MuChPoint'
summary(object)

Arguments

object

an object of class MuChPoint.

See Also

MuChPoint.

Examples

require(MuChPoint)
mu=c(rep(c(rep(1,25),rep(0,25)),3))%*%t(rep(c(rep(0,25),rep(1,25)),3))
Y=matrix(rnorm(150^2,0,2),150)+mu+t(mu)
Y=as.matrix(Matrix::forceSymmetric(Y))
res=MuChPoint(Y)
summary(res)