masterSnps {GGtools} | R Documentation |
visualize a multiGwSnpScreenResult
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, ...)
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() |
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
a list with self-describing elements
VJ Carey <stvjc@channing.harvard.edu>
if (require("GGdata")) { data(fheadFits) mm7 = masterSnps(fheadFits, minl10=7, pal=rainbow(10)) }