rhcoclust function performs robust hierarchical co-clustering between row and column entities of a data matrix by reducing the influence of outlying observations. It can be used to explore biomarker genes those are divided into upregulatory and downregulatory groups by the influence of different chemical compounds groups more accurately. It can also provide the statistical significance of the identified co-clusters. See Hasan et al., (2020). Development of the R package rhcoclust is at https://github.com/mdbahadur/rhcoclust, and official releases are available on CRAN: https://cran.r-project.org/web/packages/rhcoclust/index.html
References:
First install the R package devtools available on CRAN, if it is not
already installed. This package provides function
install_github() that enables installing packages directly
from github with the following command.
Invoke R and then type with the following command:
R> install.packages ("devtools") R> library (devtools) # install R packages that rhcoclust depends on before running the next line # see details below R> install_github ("mdbahadur/rhcoclust")
rhcoclust depends on several R packages from CRAN and from Bioconductor.
It is likely that some of these packages are not installed on your
computer. If the R package is available on CRAN, you may use the
following command line for installation (change packagename to
the name of the package to be installed, e.g, spam, maps, etc.) before
running function install_github:
R> install.packages ("packagename")
The following Bioconductor packages also need to be installed before
running function install_github or
install.packages:
R> if (!requireNamespace ("BiocManager", quietly = TRUE)) install.packages ("BiocManager") R> BiocManager::install ('spam') R> BiocManager::install ('maps')
### 2. Installation from the source of a released package.
Download the package source rhcoclust_xxx.tar.gz.
In Terminal, navigate to the directory where the package is stored,
and run the following command line:
bash $ R CMD INSTALL rhcoclust_xxx.tar.gz Again, you may
need to first install the Bioconductor packages that rhcoclust depends
on using the instructions above. Alternatively, you may also run the
following command line in R, after changing the working directory to
where rhcoclust_xxx.tar.gz is stored on your computer:
R> install.packages ("rhcoclust_xxx.tar.gz", repos = NULL, type="source")
### 3. Installation from CRAN.
Official releases are available on CRAN. To install,
R> install.packages ("rhcoclust")After installation, load the rhcoclust package into R:
R> library (rhcoclust) Bring up the documentation of the
package: R> library (help=rhcoclust)