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) |