xQTLbiolinks (version 1.6.2)

xQTLvisual_coloc: Heatmap plot of the LD-p-value relationship of the eQTL

Description

Heatmap plot of the LD-p-value relationship of the eQTL

Usage

xQTLvisual_coloc(
  gene = "",
  geneType = "auto",
  variantName = "",
  variantType = "auto",
  tissueLabels = "",
  study = "",
  population = "EUR"
)

Value

A list containing a data.table object and a ggplot object

Arguments

gene

(character) gene symbol or gencode id (versioned or unversioned are both supported).

geneType

(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".

variantName

(character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38".

variantType

(character) options: "auto", "snpId" or "variantId". Default: "auto".

tissueLabels

(a character vector) can be listed with ebi_study_tissues. If is null, use all tissue / cell-types. (Default)

study

(character) Studies can be listed using ebi_study_tissues. If is null, use all studies (Default).

population

(string) One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'.

Examples

# \donttest{
heatmapQTL <- xQTLvisual_coloc( gene="MMP7", variantName="rs11568818", study="TwinsUK")
# }