plot_manhattan_gwas: Manhattan plot for variants found in GWAS

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Manhattan plot for variants found in GWAS

Description

Display a manhattan plot. Only the variants related to the traits given as parameter will be displayed. The two horizontal lines on the plot correspond to the "suggestive" and "significant" thresholds in genome wide studies.

Usage

plot_manhattan_gwas(traits, gwas_cat, list_chr)

Arguments

traits	a vector with the trait of interest (as characters). The list of available traits can be obtained with list_gwas_traits
gwas_cat	a gwaswloc object obtained from create_gwas
list_chr	(optional) a list of chromosome to plot. (format: "chr1-22-X-Y)

Value

nothing (just display the plot)

References

Lander E, Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet. 1995;11(3):241-7.

Examples

gwas_cat <- create_gwas()

plot_manhattan_gwas(gwas_cat = gwas_cat, traits = c("Type 1 diabetes", "Type 2 diabetes"))

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.