locuscompare: Make a locuscompare plot.

In boxiangliu/locuscomparer: locuscomparer: Visualization of GWAS-QTL Colocalization Events

Make a locuscompare plot.

Description

Make a locuscompare plot.

Usage

locuscompare(in_fn1, in_fn2, marker_col1 = "rsid", pval_col1 = "pval",
  title1 = "eQTL", marker_col2 = "rsid", pval_col2 = "pval",
  title2 = "GWAS", snp = NULL, population = "EUR", combine = TRUE,
  legend = TRUE, legend_position = c("bottomright", "topright",
  "topleft"), lz_ylab_linebreak = FALSE, genome = c("hg19", "hg38"))

Arguments

in_fn1	(string) Path to the input file for study 1.
in_fn2	(string) Path to the input file for study 2.
marker_col1	(string, optional) Name of the marker column. Default: 'rsid'.
pval_col1	(string, optional) Name of the p-value column. Default: 'pval'.
title1	(string) The title for the x-axis.
marker_col2	(string, optional) Name of the marker column. Default: 'rsid'.
pval_col2	(string, optional) Name of the p-value column. Default: 'pval'.
title2	(string) The title for the y-axis.
snp	(string, optional) SNP rsID. If NULL, the function will select the lead SNP. Default: NULL.
population	(string, optional) One of the 5 popuations from 1000 Genomes: 'AFR', 'AMR', 'EAS', 'EUR', and 'SAS'. Default: 'EUR'.
combine	(boolean, optional) Should the three plots be combined into one plot? If FALSE, a list of three plots will be returned. Default: TRUE.
legend	(boolean, optional) Should the legend be shown? Default: TRUE.
legend_position	(string, optional) Either 'bottomright','topright', or 'topleft'. Default: 'bottomright'.
lz_ylab_linebreak	(boolean, optional) Whether to break the line of y-axis of the locuszoom plot.
genome	(string, optional) Genome assembly, either 'hg19' or 'hg38'. Default: 'hg19'.

Examples

in_fn1 = system.file('extdata','gwas.tsv', package = 'locuscomparer')
in_fn2 = system.file('extdata','eqtl.tsv', package = 'locuscomparer')
locuscompare(in_fn1 = in_fn1, in_fn2 = in_fn2)

boxiangliu/locuscomparer documentation built on Nov. 27, 2022, 7:26 a.m.