GWAF (version 2.0)

GWplot: function for making genome-wide p-value 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)

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-value 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.