manhattanPlot: produce a manhattan plot for a given study, based on specific...

In vjcitn/gwaslake: Workshop for exploring MRC IEU GWAS analysis ecosystem with Bioconductor

produce a manhattan plot for a given study, based on specific coordinates or gene symbol with radius for flanking region

Description

produce a manhattan plot for a given study, based on specific coordinates or gene symbol with radius for flanking region

Usage

manhattanPlot(
  studyID = "ubm-a-524",
  symbol = "BCAN",
  start = NULL,
  stop = NULL,
  chromosome = NULL,
  radius = 0,
  datasource = gwidf_2021_01_30
)

Arguments

studyID	character(1) id of study in ieugwasr::gwasinfo() catalog, defaults to "ubm-a-524", which is a study described in Elliott et al Nature October 2018
symbol	a gene symbol (to be used with genesym_to_string, implicitly); if absent, chromosome, start and end must be supplied, defaults to 'BCAN'
start	chromosomal address to start region (will have radius subtracted if supplied)
stop	chromosomal address to end region (will have radius added if supplied)
chromosome	name of chromosome in Ensembl nomenclature (e.g., 1, 2, ...)
radius	numeric default to zero, specifies flanking region
datasource	data.frame that includes study identifier id and trait for labeling

Examples

manhattanPlot(radius=500000)

vjcitn/gwaslake documentation built on Aug. 9, 2022, 5:45 p.m.