mhplot: Manhattan Plot for meta-analysis results

In MultiMeta: Meta-analysis of Multivariate Genome Wide Association Studies

Description

mhplot returns a pdf file containing the Manhattan plot of meta-analysis results.

Usage

  mhplot(res.file = NULL, data = NULL,
    col = c("darkgrey", "lightgrey"),
    out.file = "mhplot.pdf", main = "MHplot",
    plab = "p_value", CHRlab = "chr", POSlab = "Position",
    sig.p = 5e-08, sug.p = 5e-07, sep = " ")

Arguments

res.file	File name for the file(s) containing meta-analysis results. For multiple files (e.g. one file for each chromosome) the special character "*" is allowed. This is an alternative to data.
data	Dataset containing meta-analysis results. This is an alternative to file, if results are already loaded in the R workspace.
col	Choice of two colours for the plot. They will be alternating for different chromosomes.
out.file	File name for the output.
main	Title to appear on plot.
plab	p-values label i.e. column name for the p-values column.
CHRlab	Chromosome label i.e. column name for the chromosome numbers column.
POSlab	Position label i.e. column name for the position numbers column.
sig.p	Significant p-values level.
sug.p	Suggestive p-values level.
sep	Separator used in file. Default is white space.

Details

The function is useful for a quick overview of meta-analysis results. Two different types of input are allowed:

• a data frame containing chromosome, position and p-values to be plotted.

• a file name for retrieving information from file. Note that separator is set to white space, can be changed accordingly if needed. Special character "*" is allowed for selecting more than one file (e.g. in case there is one file for each chromosome).

Value

The output is a pdf file containing the Manhattan Plot.

MultiMeta documentation built on May 2, 2019, 9:11 a.m.