masterSnps {GGtools}R Documentation

visualize a multiGwSnpScreenResult

Description

visualize a multiGwSnpScreenResult

Usage

masterSnps(mgw, n = 50, auto = TRUE, orgdb = "org.Hs.eg.db", minl10 = 5, 
gstart = 0, gend = 3e+09,
genomesize = 3e+09, pcex = 1, pal = rainbow(20), numxax=FALSE, ...)

Arguments

mgw a multiGwSnpScreenResult, for example from gwSnpTests with a GeneSet on lhs of formula
n number of best snps to retain per gene
auto restrict attention to autosomes?
orgdb an annotation library like org.Hs.eg.db
minl10 threshold of -log10 p above which we keep SNP for plotting
gstart position at which genome-wide SNP locations begin
gend position at which genome-wide SNP locations end
genomesize number of bases over which plotting will be conducted (e.g., ylim=c(0, genomesize) )
pcex cex setting for pch of plot
pal a palette to differentiate gene coloring
numxax logical: if TRUE, x axis labels genomic coordinates, otherwise chromosome
... args passed to plot()

Details

experimental display with snp location as ordinate and gene location as abscissa – point plotted if snp is associated with gene at p smaller than the threshold specified

Value

a list with self-describing elements

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

if (require("GGdata")) {
 data(fheadFits)
 mm7 = masterSnps(fheadFits, minl10=7, pal=rainbow(10))
 }

[Package GGtools version 3.2.0 Index]