do_coloc: Run colocalisation analyses

In jwr-git/mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

Run colocalisation analyses

Description

Runs colocalisation using any of the following methods:

1. Coloc.abf, see coloc::coloc.abf()

2. Coloc.susie, see coloc::coloc.susie()

3. PWCoCo, see PWCoCo

NB: PWCoCo is not available on Windows.

Usage

do_coloc(
  dat,
  cdat = NA,
  method = "coloc.abf",
  coloc_window = 5e+05,
  plot_region = F,
  bfile = NULL,
  plink = NULL,
  pwcoco = NULL,
  workdir = tempdir(),
  cores = 1,
  verbose = TRUE
)

Arguments

dat	A data.frame of harmonised data
cdat	A named list of regional data but can be omitted (Optional)
method	Which method of colocalisation to use: coloc.abf, coloc.susie, pwcoco (Optional)
coloc_window	Size (+/-) of region to extract for colocalisation analyses (Optional)
plot_region	Whether to plot the regions or not
bfile	Path to Plink bed/bim/fam files (Optional)
plink	Path to Plink binary (Optional)
pwcoco	If PWCoCo is the selected coloc method, path to PWCoCo binary (Optional)
workdir	Path to save temporary files (Optional)
cores	Number of cores for multi-threaded tasks (Optional) NB: Unavailable on Windows machines
verbose	Display verbose information (Optional, boolean)

Value

A data.frame of colocalistion results

See Also

[coloc::coloc.abf()], [coloc::coloc.susie()]

jwr-git/mrpipeline documentation built on Oct. 2, 2022, 3:41 p.m.