Manhattan.plot {CGEN}R Documentation

Manhattan plot

Description

Creates a Manhattan plot

Usage

 Manhattan.plot(infile, plot.vars, locusMap.list, op=NULL)

Arguments

infile

Output file from GxE.scan. No default.

plot.vars

Character vector of the variables in infile to plot. These variables should p-values. No default.

locusMap.list

See locusMap.list. No default.

op

List of options (see details). The default is NULL.

Details

Plots p-values on a minus log base 10 scale versus the locations of the SNPs on each chromosome.

Options list op: Below are the names for the options list op. All names have default values if they are not specified.

Value

Returns nothing. Creates a Manhattan plot.

See Also

QQ.plot, locusMap.list

Examples

 
# Load the data containing the chromosomes and locations
data(LocusMapData, package="CGEN") 

# For illustrative purposes, add some hypothetical p-values to x
# set.seed(123)
LocusMapData[, "pvalue"] <- runif(nrow(LocusMapData))

# Define the input list locusMap.list
locusList <- list(snp.var="SNP", chrm.var="CHROMOSOME", loc.var="LOCATION")

# Create the plot
Manhattan.plot(LocusMapData, "pvalue", locusList)


[Package CGEN version 3.29.0 Index]