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Installation Dependencies
Before installing plotVCF make sure you have devtools and BiocManager R packages installed in your current R library, otherwise you will not be able to install it.
In order to ensure this you can run these two commands:
if (!require("devtools")) install.packages("devtools")
if (!require("BiocManager")) install.packages("BiocManager")
R will check for these packages presence in your local library and, if not found, it will proceed installing them.
It may take a while, be patient, you need to install those just once.
It is a good idea to periodically run those commands to see if an updated version of BiocManager has been released. In case, you will be presented with a message such as:
if (!require("BiocManager")) install.packages("BiocManager")
Loading required package: BiocManager
Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10r83330)
Bioconductor version '3.15' is out-of-date; the current release version '3.16'
is available with R version '4.2'; see https://bioconductor.org/install
I strongly suggest you to update BiocManager anytime an updated version is available (take a look here for updated information). Just pass the correct version to the install command (in the case presented above version 3.16):
BiocManager::install(version = "3.16")
It will also ask you if you want to upgrade your packages to the updated version of BiocManager, which I strongly recommend as well:
Upgrade 68 packages to Bioconductor version '3.16'? [y/n]: y
It will take a while but again, you only need to perform this once in a while and actually upgrade when a new BiocManager version is available 😉