All functions

compute_pca()

Compute the genomic components (and some figures) for ethnicity based on VCF files.

estimate_ethnicity()

Format VCF files and compute the genomic components (and some figures) for ethnicity.

ggheatmap()

Compute heatmap with dendrogram on x-axis and y-axis using ggplot2.

pca_report()

Compute an analysis report using principal component analysis from flashpca tool.

qc_idats()

Compute quality-control of methylation array from Illumina using a rmarkdown template.

qc_impute()

Compute post-imputation quality-control report using a default rmarkdown template.

qc_plink()

Compute quality-control of genotyping array (PLINK format) using a rmarkdown template.

read_idats()

Efficiently import idats files mostly using minfi functions.