# Install CARoT from CRAN:
install.packages("CARoT")
# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("umr1283/CARoT")
library(CARoT)
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#> ── Attaching packages ────────────────────────────────────────── CARoT 0.10.0 ──
#> ✓ rain 0.5.0 ✓ dmapaq 0.3.4
#> ✓ dgapaq 0.6.1
#>
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 from other packages:
rain
MiSTr
MiSTr::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.
dgapaq
dgapaq::qc_plink()
allows to compute quality-control of genotyping array (PLINK format) using a Rmarkdown template.dgapaq::qc_vcf()
allows to compute post-imputation quality-control report using a default Rmarkdown template.
dmapaq
dmapaq::ggheatmap()
allows to compute heatmap with dendrogram on x-axis and y-axis using ggplot2.dmapaq::read_idats()
allows to efficiently import idats files mostly using minfi functions.dmapaq::qc_idats()
allows to compute quality-control of methylation array from Illumina using a 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.