MA-plot from base means and log fold changes

Description

Visualize the comparison between the rates calculated from two different INSPEcT objects profiled in steady-state conditions.

Usage

## S4 method for signature 'INSPEcT_diffsteady'
plotMA(object, ...)

Arguments

Details

Possible arguments to "plotMA":

• "rate" - A character, which represent the rate to be visualized, either "synthesis", "processing" or "degradation". By default, "synthesis" is chosen.

• "alpha" - A numeric, The confidence interval for significance (FDR), by default 0.1

• "xlim" - A numeric vector of length 2, limits of x-axis, by default the range of the data.

• "xlab" - A character, the label of x-axis, by default "log2 geometric mean"

• "ylim" - A numeric vector of length 2, limits of y-axis, by default the range of the data.

• "ylab" - A character, the label of y-axis, by default "log2 fold change"

• "main" - A character, the title of the plot, by default the name of the visualized rate.

See Also

http://en.wikipedia.org/wiki/MA_plot

Examples

data('simData3rep', package='INSPEcT')
data('simData3rep_2', package='INSPEcT')
diffrates <- compareSteady(simData3rep, simData3rep_2)
plotMA(diffrates, alpha=.5)

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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> library(INSPEcT)
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: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/INSPEcT/plotMA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMA
> ### Title: MA-plot from base means and log fold changes
> ### Aliases: plotMA plotMA,INSPEcT_diffsteady-method
> 
> ### ** Examples
> 
> data('simData3rep', package='INSPEcT')
> data('simData3rep_2', package='INSPEcT')
> diffrates <- compareSteady(simData3rep, simData3rep_2)
> plotMA(diffrates, alpha=.5)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>