In mcanouil/CARoT: Centralised and Automated Reporting Tools

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Centralised and Automated Reporting Tools


Installation

# Install CARoT from CRAN:
install.packages("CARoT")

# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("umr1283/CARoT")

library(CARoT)

Overview

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

  • rain::estimate_ethnicity() allows to format VCF files and compute the genomic components (and some figures) for ethnicity using flashpca software
  • rain::pca_report() allows to compute an analysis report using principal component analysis from flashpca software.

• 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.

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.

mcanouil/CARoT documentation built on Sept. 18, 2021, 4:43 a.m.