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.
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.
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.