Plotting function for gene means and standard deviations

Description

Plots the row standard deviation of a matrix of expression data against the row mean, or the rank of the row mean.

Usage

plotMeanSD(indata, by.rank = TRUE, line = FALSE, ymax = NULL)

Arguments

Details

Generates a scatter plot of the row standard deviations of a matrix of expression data against the row means or ranks of the row means.

Value

NULL

Author(s)

Rachel Chen and Blythe Durbin-Johnson

Examples

library(LMGene)
library(Biobase)

data(sample.eS)
# transform data
trans.eS <- transeS(sample.eS, lambda = 727, alpha = 56)

# plot SD against rank of mean
plotMeanSD(trans.eS, line = TRUE)
plotMeanSD(sample.eS, line = TRUE, ymax = 1000)

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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'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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> library(LMGene)
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: multtest
Loading required package: survival
Loading required package: affy

Attaching package: 'LMGene'

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

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LMGene/plotMeanSD.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMeanSD
> ### Title: Plotting function for gene means and standard deviations
> ### Aliases: plotMeanSD
> ### Keywords: dplot
> 
> ### ** Examples
> 
> library(LMGene)
> library(Biobase)
> 
> data(sample.eS)
> # transform data
> trans.eS <- transeS(sample.eS, lambda = 727, alpha = 56)
> 
> # plot SD against rank of mean
> plotMeanSD(trans.eS, line = TRUE)
> plotMeanSD(sample.eS, line = TRUE, ymax = 1000)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>