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xQTLbiolinks (version 1.6.2)

xQTLvisual_locusCombine: Generate a combined figure including locusZoom and locuscompare plot

Description

This function is rebuilt from locuscompare.R (https://github.com/boxiangliu/locuscomparer/blob/master/R/locuscompare.R).

Usage

xQTLvisual_locusCombine(
  gwasEqtldata,
  posRange = "",
  population = "EUR",
  highlightSnp = "",
  legend_position = "bottomright",
  snpLD = NULL
)

Value

A ggplot object.

Arguments

gwasEqtldata

A data.frame or a data.table that including signals from both GWAS and eQTL. Five columns are required (arbitrary column names is supported):

Col 1. "snps" (character), using an rsID (e.g. "rs11966562").

Col 2. "chromosome" (character), one of the chromosome from chr1-chr22.

Col 3. "postion" (integer), genome position of snp.

Col 4. "P-value" (numeric) of GWAS signals.

Col 5. "P-value" (numeric) of eQTL signals.

posRange

Genome range that you want to visualize (e.g. "chr6:3e7-7e7"). Default is the region that covers all snps.

population

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

highlightSnp

Default is the snp that with lowest p-value.

legend_position

(string, optional) Either 'bottomright','topright', or 'topleft'. Default: 'bottomright'.

snpLD

A data.frame object of LD matrix. Default is null.