Package index • topr

All functions

CD_FINNGEN: Finngen r7 Crohn‘s disease (K11_CROHNS)

CD_UKBB: UKBB Crohns disease (ICD 10 code K50)

R2_CD_UKBB: Example dataset including the R2 column for the locuszoom plot function

UC_UKBB: UKBB Ulcerative colitis (ICD 10 code K51)

annotate_with_nearest_gene(): Get the nearest gene for one or more snps

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

effect_plot(): Create a plot comparing effects within two datasets

effectplot(): Create a plot comparing variant effects in 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_snps_within_region(): Get SNPs/variants within region

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_top_snp(): Get the top hit from the dataframe

get_topr_colors(): 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

regionplot(): Create a regionplot

topr-package topr: topr