Package index • panvaR

Formatting Inputs

“Functions for standardizing inputs and organizing files”

set_out_dir(): Set path for output files
set_panvar_prefix(): sets global option "panvar_prefix" for output directory of intermediate panvar files. If not supplied will be sent to output of 'tempdir()'.
set_plink_path(): Set path to plink2 executable
make_panvar_inputs(): Make standard inputs for panvaR
snp_qc_plink(): Quality control a snp file using plink2
format_snpeff_annotations(): Extracts snpeff annotations from vcf

“Functions for generating information about snps and integrating results”

get_ld_in_window(): Get linkage disequilibrium
make_panvar_tables(): Make some standardized tables from gwas and annotation tables
make_scores(): Make scores
panvar_mvp_gwas(): Use rMVP to run gwas
snp_make_clumps(): Assign snps to clumps based on LD after gwas
get_chrom_from_id(): Extract chromsome from marker.ID in the form "CHR-POS"
get_bp_from_id(): Extract position from marker.ID in the form "CHR-POS"

“Functions for visualizing results”

plot_effect(): Make volcano style effect size vs pvalue plot
plot_gene_annotation(): Plot genes and their locations
plot_panvar(): Make a plot that lines up manhattan and gene locations
plot_panvar_manhattan(): Make sideways manhattan plot for building locus zoom. Receives output from a single gwas model.
plot_pc_scree(): Calculate and plot pcs
make_consistent_scale(): Generate discrete scale

“Functions for running the shiny app”

panvar_gui(): panvar_gui Run the panvaR shiny implementation. Will launch in a default browser or can navigate to IP address shown.