Man pages for topr
Create Custom Plots for Viewing Genetic Association Results
| 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... |
| 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_gene_coords | 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_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... |
| 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... |
| 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 |
| pipe | Pipe operator |
| qqtopr | Create a quantile quantile (QQ) plot |
| R2_CD_UKBB | Example dataset including the R2 column for the locuszoom... |
| regionplot | Create a regionplot |
| topr | topr |
| UC_UKBB | UKBB Ulcerative colitis (ICD 10 code K51) |
