| 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, |
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, |
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 |
Slots
Sa vector object of type
numeric, giving the values of the statistics S_n(n_1,...,n_L) following the number L.Na numeric vector with the position of the different break-points.
btan 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 |
y |
used for S4 compatibility represented the matrix (typically,
the matrix used in the program |
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 |
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 |
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 |
See Also
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)