| manhattan {otargen} | R Documentation |
Retrieve GWAS summary statistics to create a Manhattan plot
Description
This function retrieves summary statistics for a given GWAS study ID, which are used to generate a Manhattan plot.
The Manhattan plot is a graphical representation of genetic association studies, particularly in genome-wide association studies (GWAS).
It displays the results of statistical associations between genetic variants and a trait or disease of interest across the genome.
This function returns a data frame of the underlying data, which can be used to recreate the Manhattan plot using the plot_manhattan() function,
or for custom plots and downstream analysis.
Usage
manhattan(study_id, pageindex = 0, pagesize = 100)
Arguments
study_id |
Character: Open Targets Genetics generated ID for the GWAS study. |
pageindex |
Int: Index of the current page (pagination index >= 0). |
pagesize |
Int: Number of records in a page (pagination size > 0). |
Value
Returns a data frame containing the Manhattan associations for the input study ID. The table consists of the following columns:
pval_mantissa: Numeric vector. Mantissa of the p-value.pval_exponent: Integer vector. Exponent of the p-value.credible_set_size: Integer vector. Size of the credible set.ld_set_size: Integer vector. Size of the LD set.total_set_size: Integer vector. Total size of the set.pval: Numeric vector. P-value.odds_ratio: Logical vector. Odds ratio.odds_ratio_ci_lower: Logical vector. Lower confidence interval of the odds ratio.odds_ratio_ci_upper: Logical vector. Upper confidence interval of the odds ratio.beta: Numeric vector. Beta value.beta_ci_lower: Numeric vector. Lower confidence interval of the beta value.beta_ci_upper: Numeric vector. Upper confidence interval of the beta value.direction: Character vector. Direction of the effect.best_genes_score: Numeric vector. Score of the best genes.best_genes_gene_id: Character vector. Gene ID of the best genes.best_genes_gene_symbol: Character vector. Gene symbol of the best genes.best_coloc_genes_score: Numeric vector. Score of the best colocated genes.best_coloc_genes_gene_id: Character vector. Gene ID of the best colocated genes.best_coloc_genes_gene_symbol: Character vector. Gene symbol of the best colocated genes.best_locus2genes_score: Numeric vector. Score of the best locus-to-genes.best_locus2genes_gene_id: Character vector. Gene ID of the best locus-to-genes.best_locus2genes_gene_symbol: Character vector. Gene symbol of the best locus-to-genes.variant_id: Character vector. Variant ID.variant_position: Integer vector. Variant position.variant_chromosome: Character vector. Variant chromosome.variant_rs_id: Character vector. Variant rsID.
Examples
## Not run:
result <- manhattan(study_id = "GCST90002357")
result <- manhattan(study_id = "GCST90002357", pageindex = 2, pagesize = 50)
## End(Not run)