umr1283 / dgapaq

DNA Genotyping Arrays Processing And Quality-Control

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 of samtools 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.

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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.