plotManhattan {CNVRanger} | R Documentation

## Manhattan Plot

### Description

Manhattan plot for p-values of a CNV-GWAS

### Usage

    plotManhattan(all.paths, regions, chr.size.order, plot.pdf = FALSE)

### Arguments

`all.paths` | Object returned from `CreateFolderTree` function with the working folder tree
`regions` | `GRanges` as returned by `cnvGWAS`
`chr.size.order` | `data.frame` with two columns: (i) 'chr': chromosome names (character), and (ii) 'size': length of the chromosomes in bp (integer). A `GRanges` containing one chromosome per range can be used instead (the chromosomes should be in the expected order).
`plot.pdf` | Logical plot a to pdf file

### Value

Plots to graphics device.

### Author(s)

Vinicius Henrique da Silva <vinicius.dasilva@wur.nl>

### Examples

    # Load phenotype-CNV information
    data.dir <- system.file("extdata", package="CNVRanger")

    phen.loc <- file.path(data.dir, "Pheno.txt")
    cnv.out.loc <- file.path(data.dir, "CNVOut.txt")
    map.loc <- file.path(data.dir, "MapPenn.txt")

    phen.info <- setupCnvGWAS('Example', phen.loc, cnv.out.loc, map.loc)
    all.paths <- phen.info$all.paths
    segs.pvalue.gr <- cnvGWAS(phen.info)

    # Define the chromosome order in the plot
    order.chrs <- c(1:24, "25LG1", "25LG2", 27:28, "LGE22", "1A", "4A")

    # Chromosome sizes
    chr.size.file <- file.path(data.dir, "Parus_major_chr_sizes.txt")
    chr.sizes <- scan(chr.size.file)
    chr.size.order <- data.frame(chr=order.chrs, sizes=chr.sizes, stringsAsFactors=FALSE)

    # Plot Manhatthan to a pdf within the 'Results' workfolder
    plotManhattan(all.paths, segs.pvalue.gr, chr.size.order)

[Package CNVRanger version 1.8.0 Index]