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topr (version 2.0.1)

Create Custom Plots for Viewing Genetic Association Results

Description

A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.

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Install

install.packages('topr')

Monthly Downloads

730

Version

2.0.1

License

LGPL (>= 3)

Issues

7

Pull Requests

0

Stars

60

Forks

15

Maintainer

Thorhildur Juliusdottir

Last Published

March 15th, 2024

Functions in topr (2.0.1)

get_snps_within_region

Get SNPs/variants within region
match_alleles

Match the variants in the snpset by their alleles
manhattan

Create a Manhattan plot
regionplot

Create a regionplot
match_by_alleles

Match the variants in the snpset by their alleles
get_topr_colors

Get the top hit from the dataframe
qqtopr

Create a quantile quantile (QQ) plot
get_top_snp

Get the top hit from the dataframe
locuszoom

Create a locuszoom-like plot
topr

topr
%>%

Pipe operator
match_by_pos

Get variants that overlap between two datasets
flip_to_positive_allele_for_dat1

Flip to the positive allele for dataset 1
annotate_with_nearest_gene

Get the nearest gene for one or more snps
effectplot

Create a plot comparing variant effects in two datasets
create_snpset_code

Show the code/functions used to create a snpset
create_snpset

Create a dataframe that can be used as input for making effect plots
CD_FINNGEN

Finngen r7 Crohn‘s disease (K11_CROHNS)
UC_UKBB

UKBB Ulcerative colitis (ICD 10 code K51)
effect_plot

Create a plot comparing effects within two datasets
get_best_snp_per_MB

Get the index/lead variants
get_lead_snps

Get the index/lead variants
get_genes_in_region

Get SNPs/variants within region
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_gene_coords

Get the genetic position of a gene by gene name
CD_UKBB

UKBB Crohns disease (ICD 10 code K50)
R2_CD_UKBB

Example dataset including the R2 column for the locuszoom plot function
get_snpset_code

Show the code/functions used to get a snpset
get_snpset

Create a dataframe that can be used as input for making effect plots
get_overlapping_snps_by_pos

Get variants that overlap between two datasets