plotLDarc: LocusExplorer - LDarc plot

In oncogenetics/oncofunco: Custom function for Oncogenetics team

LocusExplorer - LDarc plot

Description

LD Arc plot for LocusExplorer.

Usage

plotLDarc(
  LD = NULL,
  xStart = NULL,
  xEnd = NULL,
  upper = NULL,
  lower = NULL,
  statNames = c("Stepwise", "JAM"),
  minR2 = 0.4,
  hitsOnly = FALSE,
  pad = TRUE,
  title = NULL
)

Arguments

LD	plink LD output format, data.frame object with c("BP_A","SNP_A","BP_B","SNP_B","R2") columns.
xStart, xEnd	Region range, zoom, minimum BP and maximum BP, advised to keep this less than 5Mb.
upper, lower	SNP names to label in the plot. Must be present in assoc data.frame.
statNames	Two statistics methods name used for y-axis, string, default c("Stepwise", "JAM").
minR2	Filter LD on minimum R2, filter out "non-significant" relationships.
pad	Default is TRUE, to align plots pad strings with spaces, using oncofunco::strPadLeft().
title	character string for plot title. Default is NULL, i.e.: no plot title.

Value

a ggplot object

Author(s)

Tokhir Dadaev

oncogenetics/oncofunco documentation built on March 9, 2024, 5:23 p.m.