GWplot {GWAF}R Documentation

function for making genome-wide p-values plot

Description

GWplot function plots -log_{10} p-value based on SNP's chromosomal position in bitmap format.

Usage

GWplot(data, pval, pos, chr, chr.plot=c(1:22,"X"), title.text="", 
ylim=Inf, outfile, cutoff1=5e-08, cutoff2=4e-07)

Arguments

data a dataframe that contains p-values, chromosome number and physical position of SNPs
pval a character string correspong to the name of the p-value column
pos a character string correspong to the name of column with SNP physical positions
chr a character string correspong to the name of column with SNP chromosome number
chr.plot the chsomosomes of interest for GWplot; either 1:22 or c(1:22,"X"), default chr.plot=c(1:22,"X"), "X" for X chromosome
title.text the title of the genome-wide p-value plot
ylim the maximum of -log_{10} p-value to be plotted, useful when not want to plot extremely small p-values
outfile the file name (xxxx.bmp) for output plot in bitmap format
cutoff1 genome-wide significance; default is 5E-8 ; p-values below this threshold will be highlighted in red
cutoff2 suggestive genome-wide significance; default is 4E-7; p-values below this threshold but above cutoff1 will be highlighted in blue

Details

When the dataset has 0 p-value, GWplot will generate pvalzero.csv that contain the results with 0 p-value and make the genome-wide p-values plot by replacing 0 p-value with 5E-324. P-values that reach genome-wide significance are displayed in red color; P-values that reach suggestive genome-wide significance but not genome-wide significance are displayed in blue color.

Author(s)

Qiong Yang <qyang@bu.edu> and Ming-Huei Chen <mhchen@bu.edu>


[Package GWAF version 1.2 Index]