# Create Custom Plots for Viewing Genetic Association Results

## 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)