README.md

In cgrace1978/manhplot: The Manhattan++ Plot

MANHATTAN++

MANHATTAN++ is software to generate a transposed manhattan heatmap, implemented in R.

Getting Started

You need to install the latest version of R The R package can be run on Windows and Linux, you must specify paths to the filenames you are using as input and output.

To install the software from the GIT repository:

install.packages("devtools")
library(devtools)

install_github("cgrace1978/manhplot", dependencies = T, force = T)

The following command will run the plot with default data in the package. The pdf (test.pdf) will be created in the current working directory in R (This can be viewed using the getwd() command):

library(manhplot)

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

## Run manhattan++ with the default paramaters and files included in the package
manhplusplot(infile = infile,outfile = "test", configfile = configfile, snpfile = snpfile)

For more information on using manhattan++ please visit the Manhattan++ wiki

Citation

To use Manhattan++ please cite the following paper:

Grace et al

Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers

BMC Bioinformatics 2019; 20(1):610

PubMed: 31775616

cgrace1978/manhplot documentation built on Feb. 3, 2023, 3:48 a.m.