# 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 compute the genomic component (and some figures) for ethnicity based on VCF files.
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 with
results="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.
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