# Install CARoT from CRAN:
install.packages("CARoT")
# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("mcanouil/CARoT")
CARoT (Centralised and Automated Reporting Tools) is an under development set of Quality-Control reporting tools and some other functions.
Currently CARoT includes the following functions:
estimate_ethnicity()
allows to format VCF files and compute the genomic components (and some figures) for ethnicity.ggheatmap()
allows to compute heatmap with dendrogram on x-axis and y-axis using ggplot2.read_idats()
allows to efficiently import idats files mostly using minfi functions.pca_report()
allows to compute an analysis report using principal component analysis from flashpca tool.
The function can be used in a chunk within a Rmarkdown document/script withresults="asis"
to render the report.qc_idats()
allows to compute quality-control of methylation array from Illumina using a rmarkdown template.qc_plink()
allows to compute quality-control of genotyping array (PLINK format) using a rmarkdown template.qc_impute()
allows to compute post-imputation quality-control report using a default rmarkdown template.
If you encounter a clear bug, please file a minimal reproducible example
on github.
For questions and other discussion, please contact the package
maintainer.
Please note that this project is released with a Contributor Code of
Conduct.
By participating in this project you agree to abide by its terms.