plotRegion: A Flexible Function for Manhattan Plot

In LeileiCui/ADDO: a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci

Description

Plot the GWAS results for a single trait on one particular chromosome, or specific region on one chromosome

Usage

plotRegion(chrs = chrs, traitIdx = 1, alldat = alldat, from = NULL,
  to = NULL, main = "", ldinfo = ldinfo, ylim = NULL,
  cex_points = 2.5, cex_points_peak = 4, cex_lab = 1.3,
  cex_axis = 1.3, cex_main = 1.4)

Arguments

chrs	A vector of numbers or characters indicating the chromosomes of markers.
traitIdx	A numeric variable indicating the index of trait to plot.
alldat	A dataframe with columns containing SNP, chr, pos and association strength (-log10 P value) of markers for one or more traits.
from	A character specify the name of SNP.
to	A character specify the name of SNP.
main	A character specifies the title of the plot.
ldinfo	A data frame generated using –r2 –ld-snp command in PLINK .
ylim	A vector of two numeric variables specify the range of y axis..
cex_points	A numeric variable specify the cex of points to plot.
cex_points_peak	A numeric variable specify the cex of point for the lmost significant marker to plot..
cex_lab	A numeric value specifies the cex of labels in the plot.
cex_axis	A numeric value specifies the cex of axis in the plot.
cex_main	AA numeric value specifies the cex of title in the plot.

Value

a figure

Author(s)

Bin Yang and Leilei Cui

LeileiCui/ADDO documentation built on July 25, 2020, 1:51 a.m.