manhplusplot {manhplot}

Generate the manhattan++ plot

Description

Generate the manhattan++ plot

Usage

manhplusplot(infile, outfile, configfile, snpfile, drawastiff = F,
  GWS = 5e-08, FDR = 0.001, MAF = 0.05, chrname = "chr",
  posname = "pos", pvalname = "pvalue", frqname = "maf",
  conseqname = "conseq", showgenes = F, showrsids = F,
  pos.split = 3e+06, pval.split = 0.125, max.pval = 20)

Arguments

infile

Input GWAS summary statistics

outfile

Output file prefix for the manhattan++ plot

configfile

Configuration file

snpfile

Table of SNPs to visualize

drawastiff

If TRUE draw a Tiff file, if FALSE draw a PDF file

GWS

Genome wise significance pvalue threshold (5E-8 by default)

FDR

False discovery Rate pvalue threshold (1E-3 by default)

MAF

Minor Allele Frequency threshold

chrname

Column name for chromosome in GWAS infile

posname

Column name for position in GWAS infile

pvalname

Column name for pvalue in GWAS infile

frqname

column name for allele frequency in GWAS infile

conseqname

column name for variant annotation consequence in GWAS infile

showgenes

If T shows known genes as bubbles on main manhattan plot, if F show positions of interest as bubbles

showrsids

If showgenes is T, then show the rsids, rather than genes

pos.split

The bin lengths for positions

pval.split

The bin lengths for pvalues

max.pval

The maximum pvalue to display

Details

For file formats see github page https://github.com/cgrace1978/manhplot

Author(s)

Chris Grace

Examples

library(manhplot)
## Load R.utils for gzip functionality
library(R.utils)

## unzip the data included with this package
gunzip(system.file("extdata","cad.add.160614_manhformat.txt.gz",package = "manhplot"))

infile<-system.file("extdata","cad.add.160614_manhformat.txt",package = "manhplot")
configfile<-system.file("extdata","config.txt", package = "manhplot")
snpfile<-system.file("extdata","56cad.add.160614.variants.txt", package = "manhplot")

manhplusplot(infile = infile,outfile = file.path(tempdir(), "default-plot"), 
               configfile = configfile, snpfile = snpfile)

## zip the data
gzip(system.file("extdata","cad.add.160614_manhformat.txt",package = "manhplot"))