Package: topr 2.0.2

topr: Create Custom Plots for Viewing Genetic Association Results

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.

Authors:Thorhildur Juliusdottir [cph, aut, cre], Andri Stefansson [aut], Kyle Scott [ctb]

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topr.pdf |topr.html✨
topr/json (API)
NEWS

# Install 'topr' in R:
install.packages('topr', repos = c('https://totajuliusd.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/totajuliusd/topr/issues

Datasets:
  • CD_FINNGEN - Finngen r7 Crohn‘s disease
  • CD_UKBB - UKBB Crohns disease
  • R2_CD_UKBB - Example dataset including the R2 column for the locuszoom plot function
  • UC_UKBB - UKBB Ulcerative colitis

On CRAN:

6.77 score 47 stars 29 scripts 2.0k downloads 27 exports 41 dependencies

Last updated 21 days agofrom:319cb0adb5. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 16 2024
R-4.5-winOKOct 16 2024
R-4.5-linuxOKOct 16 2024
R-4.4-winOKOct 16 2024
R-4.4-macOKOct 16 2024
R-4.3-winOKOct 16 2024
R-4.3-macOKOct 16 2024

Exports:annotate_with_nearest_genecreate_snpsetcreate_snpset_codeeffect_ploteffectplotflip_to_positive_allele_for_dat1get_best_snp_per_MBget_geneget_gene_coordsget_genes_by_Gene_Symbolget_genes_in_regionget_lead_snpsget_overlapping_snps_by_posget_sign_and_sugg_lociget_snps_within_regionget_snpsetget_snpset_codeget_top_snpget_topr_colorslocuszoommanhattanmanhattanExtramatch_allelesmatch_by_allelesmatch_by_posqqtoprregionplot

Dependencies:clicolorspacecpp11dplyreggenshumanfansifarvergenericsggplot2ggrepelgluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Get the nearest gene for one or more snpsannotate_with_nearest_gene
Finngen r7 Crohn‘s disease (K11_CROHNS)CD_FINNGEN
UKBB Crohns disease (ICD 10 code K50)CD_UKBB
Create a dataframe that can be used as input for making effect plotscreate_snpset
Show the code/functions used to create a snpsetcreate_snpset_code
Create a plot comparing effects within two datasetseffect_plot
Create a plot comparing variant effects in two datasetseffectplot
Flip to the positive allele for dataset 1flip_to_positive_allele_for_dat1
Get the index/lead variantsget_best_snp_per_MB
Get the genetic position of a gene by gene nameget_gene
Get the genetic position of a gene by gene nameget_gene_coords
Get the genetic position of a gene by its gene nameget_genes_by_Gene_Symbol
Get SNPs/variants within regionget_genes_in_region
Get the index/lead variantsget_lead_snps
Get variants that overlap between two datasetsget_overlapping_snps_by_pos
Get the index/lead variantsget_sign_and_sugg_loci
Get SNPs/variants within regionget_snps_within_region
Create a dataframe that can be used as input for making effect plotsget_snpset
Show the code/functions used to get a snpsetget_snpset_code
Get the top hit from the dataframeget_top_snp
Get the top hit from the dataframeget_topr_colors
Create a locuszoom-like plotlocuszoom
Create a Manhattan plotmanhattan
Create a Manhattan plot highlighting genome-wide significant and suggestive locimanhattanExtra
Match the variants in the snpset by their allelesmatch_alleles
Match the variants in the snpset by their allelesmatch_by_alleles
Get variants that overlap between two datasetsmatch_by_pos
Create a quantile quantile (QQ) plotqqtopr
Example dataset including the R2 column for the locuszoom plot functionR2_CD_UKBB
Create a regionplotregionplot
toprtopr-package topr
UKBB Ulcerative colitis (ICD 10 code K51)UC_UKBB