Description Usage Arguments Details Author(s) Examples
View source: R/manhattan.heatmap.v1.R
Generate the manhattan++ plot
1 2 3 4 5 | 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)
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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 |
For file formats see github page https://github.com/cgrace1978/manhplot
Chris Grace
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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"))
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