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 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.
  • mist() allows to test for association between a set of SNPS/genes and continuous or binary outcomes by including variant characteristic information and using (weighted) score statistics.

Getting help

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.