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]