Manhattan plot.

Description

This functions performs a Manhattan plot of the p-values of a deepSNV test against the position

Usage

manhattanPlot(x, col = nt.col)

Arguments

Value

NULL.

Author(s)

Moritz Gerstung

Examples

data(HIVmix)
manhattanPlot(HIVmix)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(deepSNV)
Loading required package: parallel
Loading required package: Rhtslib
Rhtslib htslib version 1.1
Loading required package: IRanges
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: XVector
Loading required package: VGAM
Loading required package: splines
Loading required package: VariantAnnotation
Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate


Attaching package: 'deepSNV'

The following objects are masked from 'package:VGAM':

    dbetabinom, pbetabinom

The following object is masked from 'package:BiocGenerics':

    normalize

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/deepSNV/manhattanPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: manhattanPlot
> ### Title: Manhattan plot.
> ### Aliases: manhattanPlot
> 
> ### ** Examples
> 
> data(HIVmix)
> manhattanPlot(HIVmix)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>