manhattan.reflect {CpGassoc}

Create a Reflective Manhattan plot

Description

This function will produce a reflective manhattan plot for the observed P-values from an object of class "cpg" or "cpg.perm". The original analysis needs to be performed on a continuous variable (need T-statistics).

Usage

manhattan.reflect(x, cpgname, chr, pos, save.plot = NULL, file.type="pdf",
popup.pdf = FALSE, eps.size = c(15, 5), main.title = NULL, cpg.labels = NULL,
chr.list = NULL, color.list = NULL, fdr.cutoff=NULL, point.size=NULL, ...)

Arguments

x

Object of class "cpg" or "cpg.perm".

cpgname

A vector consisting of the labels for each CpG site.

chr

A vector consisting of the chromosome number for each CpG site.

pos

The map position of each CpG site within its chromosome.

save.plot

Name of the file for the plot to be saved to. If not specified, plot will not be saved.

file.type

Type of file to be saved. Can either be "pdf" or "eps". Selecting file.type="eps" will result in publication quality editable postscript files that can be opened by Adobe Illustrator or Photoshop.

popup.pdf

TRUE or FALSE. If creating a pdf file, this indicates if the plot should appear in a popup window as well. If running in a cluster-like environment, best to leave FALSE.

eps.size

Vector indicating the size of .eps file (if creating one). Corresponds to horizontal and height.

main.title

Main title to be put on the graph. If NULL one based on the analysis will be used.

cpg.labels

A character scalar of either "FDR" or "HOLM" which will label the significant sites on the manhattan plot.

chr.list

A vector listing the chromosomes to be plotted (all available chromosomes are plotted by default). The X and Y chromosomes can be denoted by 23 and 24.

color.list

A vector of custom colors to be used for each chromosomes in the manhattan plot.

fdr.cutoff

A numeric scalar between 0 and 1 to indicate what to consider FDR significant. Defaults to NULL.

point.size

The size of the points in the manhattan plot, if NULL, default to our default, where significant probes have different sizes.

...

Arguments to be passed to methods, such as graphical parameters.

Note

cpgname, chr, and pos must be sorted in the same order, so that the first cpgname[1] corresponds to chr[1] and pos[1], and so on.

Author(s)

Barfield, R.; Kilaru,V.; Conneely, K.
Maintainer: R. Barfield: <[e-mail]>

See Also

cpg.perm plot.cpg scatterplot cpg.assoc plot.cpg.perm manhattan

Examples

#Doing a Manhattan plot. First load the data:
data(samplecpg,samplepheno,annotation,package="CpGassoc")

examplemanhat<-cpg.assoc(samplecpg,samplepheno$Disease,large.data=FALSE)

manhattan.reflect(examplemanhat,annotation$TargetID,annotation$CHR,annotation$MAPINFO)