Genome-wide qq-normal and qq-gamma plots

Description

qqnormGenomeWide overlays quantile-quantile normal plots (qqnorm) for a series of genes (rows in the input matrix), to provide an overall assessment of Normality. Similarly, qqgammaGenomeWide overlays quantile-quantile gamma plots.

Note that the theoretical quantiles for z-scores under a Normal are the same for all genes, but the gamma theoretical quantiles depend on the Gamma parameter estimates for each gene and hence the theoretical quantiles are different for each gene (resulting in different x-values in each qq-plot)

Usage

qqnormGenomeWide(x, ngenes=min(1000, nrow(x)), ...)

qqgammaGenomeWide(x, ngenes=min(1000, nrow(x)), ...)

Arguments

Value

Produces a figure overlaying qq-normal or qq-gamma plots for ngenes comparing observed vs. theoretical quantiles

Author(s)

David Rossell

Examples

mu <- rnorm(100)
x <- matrix(rnorm(100*5,mu),ncol=5)

qqnormGenomeWide(x)
qqgammaGenomeWide(exp(x))

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)

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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
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Type 'q()' to quit R.

> library(casper)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

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

Welcome to Bioconductor

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

Loading required package: IRanges
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/qqnormGenomeWide.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qqnormGenomeWide
> ### Title: Genome-wide qq-normal and qq-gamma plots
> ### Aliases: qqnormGenomeWide qqnormGenomeWide,data.frame-method
> ###   qqnormGenomeWide,ExpressionSet-method qqnormGenomeWide,matrix-method
> ###   qqgammaGenomeWide qqgammaGenomeWide,data.frame-method
> ###   qqgammaGenomeWide,ExpressionSet-method
> ###   qqgammaGenomeWide,matrix-method
> ### Keywords: hplot distribution
> 
> ### ** Examples
> 
> mu <- rnorm(100)
> x <- matrix(rnorm(100*5,mu),ncol=5)
> 
> qqnormGenomeWide(x)
> qqgammaGenomeWide(exp(x))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>