knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
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# Install CARoT from CRAN: install.packages("CARoT") # Or the the development version from GitHub: # install.packages("remotes") remotes::install_github("umr1283/CARoT")
library(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 from other packages:
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::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::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.
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