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Last data update: 2014.03.03

R: Manhattan Plot for meta-analysis results

mhplot

R Documentation

Manhattan Plot for meta-analysis results

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