mxr_create_haploview_plot: Generate the Haploview Plot.

In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description

mxr_create_haploview_plot generates the haploview plot using Gabriel's algorithm.

Usage

mxr_create_haploview_plot(path_to_haploview = "", ped_file = "",
  info_file = "", max_distance_kb = 200, memory_mb = 2048,
  out_prefix = "", verbose = FALSE)

Arguments

path_to_haploview	The fullpath to the Haploview.jar.
ped_file	The fullpath to the PED file in haploview format.
info_file	The fullpath to the corresponding INFO file of the PED file.
max_distance_kb	The window size in kb of the LD block. (DEFAULT: 200)
memory_mb	The memory to set aside for the haploview run. (DEFAULT: 2048)
out_prefix	The output prefix for the generated files.
verbose	(Optional) Show verbose output. (DEFAULT=FALSE)

Details

For really large LD plots, it may be necessary to set the minimum memory footprint to greater than 2GB. The default memory setting for this function was already increased to 2GB from the default Haploview setting of 512MB.

Value

TRUE if the PLINK run completed successfully. FALSE, otherwise.

roslen/mxr documentation built on May 27, 2019, 11:32 p.m.