DNA Genotyping Arrays Processing And Quality-Control
Installation
# Install dgapaq from CRAN:
install.packages("dgapaq")
# Or the the development version from GitHub:
# install.packages("remotes")
remotes::install_github("umr1283/dgapaq")
Overview
qc_plink()
allows to compute quality-control of genotyping array (PLINK format) using a rmarkdown template.qc_vcf()
allows to compute post-imputation quality-control report using a default rmarkdown template.convert_assembly()
allows to convert VCFs to target genome assembly using the software CrossMap.compress_coverage()
allows to compress coverage file (output ofsamtools depth
) into contiguous segments based on position.create_genotype_matrix()
allows to create a genotype matrix based on VCFs.check_genotype()
allows to check missing data in genotype matrix against coverage information.tidy_vcf()
allows to correct missing genotypes in VCF using corrected genotype matrix.
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.
Code of Conduct
Please note that the dgapaq project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.