Create Custom Plots for Viewing Genetic Association Results

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Documentation for package ‘topr’ version 1.1.4

Help Pages

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_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
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)