Create Custom Plots for Viewing Genetic Association Results

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Documentation for package ‘topr’ version 2.0.2

• DESCRIPTION file.
• Package NEWS.

Help Pages

topr-package	topr
annotate_with_nearest_gene	Get the nearest gene for one or more snps
CD_FINNGEN	Finngen r7 Crohn‘s disease (K11_CROHNS)
CD_UKBB	UKBB Crohns disease (ICD 10 code K50)
create_snpset	Create a dataframe that can be used as input for making effect plots
create_snpset_code	Show the code/functions used to create a snpset
effectplot	Create a plot comparing variant effects in two datasets
effect_plot	Create a plot comparing effects within two datasets
flip_to_positive_allele_for_dat1	Flip to the positive allele for dataset 1
get_best_snp_per_MB	Get the index/lead variants
get_gene	Get the genetic position of a gene by gene name
get_genes_by_Gene_Symbol	Get the genetic position of a gene by its gene name
get_genes_in_region	Get SNPs/variants within region
get_gene_coords	Get the genetic position of a gene by gene name
get_lead_snps	Get the index/lead variants
get_overlapping_snps_by_pos	Get variants that overlap between two datasets
get_sign_and_sugg_loci	Get the index/lead variants
get_snpset	Create a dataframe that can be used as input for making effect plots
get_snpset_code	Show the code/functions used to get a snpset
get_snps_within_region	Get SNPs/variants within region
get_topr_colors	Get the top hit from the dataframe
get_top_snp	Get the top hit from the dataframe
locuszoom	Create a locuszoom-like plot
manhattan	Create a Manhattan plot
manhattanExtra	Create a Manhattan plot highlighting genome-wide significant and suggestive loci
match_alleles	Match the variants in the snpset by their alleles
match_by_alleles	Match the variants in the snpset by their alleles
match_by_pos	Get variants that overlap between two datasets
qqtopr	Create a quantile quantile (QQ) plot
R2_CD_UKBB	Example dataset including the R2 column for the locuszoom plot function
regionplot	Create a regionplot
topr	topr
UC_UKBB	UKBB Ulcerative colitis (ICD 10 code K51)