README.md

In mcanouil/CARoT: Centralised and Automated Reporting Tools

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)
#>                                                                   
#>   .oooooo.         .o.       ooooooooo.             ooooooooooooo 
#>  d8P'  `Y8b       .888.      `888   `Y88.           8'   888   `8 
#> 888              .8"888.      888   .d88'  .ooooo.       888      
#> 888             .8' `888.     888ooo88P'  d88' `88b      888      
#> 888            .88ooo8888.    888`88b.    888   888      888      
#> `88b    ooo   .8'     `888.   888  `88b.  888   888      888      
#>  `Y8bood8P'  o88o     o8888o o888o  o888o `Y8bod8P'     o888o     
#> 
#> ── Attaching packages ────────────────────────────────────────── CARoT 0.10.0 ──
#> ✓ rain   0.5.0     ✓ dmapaq 0.3.4
#> ✓ dgapaq 0.6.1
#> 

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.