fast_locusplot: Function to generate zoomed locus plots including linkage...

In roman-tremmel/ggfastman: ggfastman: ggplot2-based manhattenplots in fast and ultrafast

Function to generate zoomed locus plots including linkage diequilibrium using r2

Description

Function to generate zoomed locus plots including linkage diequilibrium using r2

Usage

fast_locusplot(
  data,
  build = "hg19",
  snp = "top",
  pop = "CEU",
  show_MAF = FALSE,
  show_regulom = FALSE,
  RDB_ranks = c(1, 2),
  color = "viridis",
  token = NULL
)

Arguments

data	A data.frame. Columns 'chr', 'pos','pvalue' and 'rsid' are required
build	Genomic build. Currently only hg19 is supported.
snp	Default: top snp with lowest pvalue is taken. Otherwise specify any rsid id included in data.
pop	a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU".
show_MAF	Show minor allele frequencies from specified 1000 Genomes population. Default = FALSE.
show_regulom	Show RegulomeDB ranks. More information at https://regulomedb.org/regulome-help. Default = FALSE.
RDB_ranks	Specify RegulomeDB ranks to show. Defaults are the most significants: 1 and 2 including subtypes a-f.
color	color scheme for R^2 values. Possible values are c("viridis","magma","inferno","plasma").
token	!!!REQUIRED!!!: Register for token at https://ldlink.nci.nih.gov/?tab=apiaccess

Value

A ggplot2 object/plot

Examples

fast_locusplot(gwas_data, token = "mytoken")

roman-tremmel/ggfastman documentation built on Feb. 20, 2024, 11:59 a.m.