MAplotHelpfile

Description

The MA plot displays the average log2 signal of the genes on the x-axis and the log2 fold changes on the y-axis. The upper plot represents a MA plot for the first level of gene expression analysis, whereas the other one refers to the second level. DEGs are color labeled. This function takes as input an object of class DEGs.

Usage

MAplot(object, outputformat="on screen",track="")

Arguments

Author(s)

Toma Tebaldi, Erik Dassi, Galena Kostoska

References

Dudoit, S, Yang, YH, Callow, MJ, Speed, TP. (2002). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sin. 12:1 111-139

See Also

DEGs TranslatomeDataset computeDEGs

Examples

data(tRanslatomeSampleData)
MAplot(limma.DEGs, outputformat="on screen",track="")

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(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
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 object is masked from 'package:limma':

    plotMA

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: Biobase
Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    anyMissing, rowMedians

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

Loading required package: org.Hs.eg.db

Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots

Attaching package: 'gplots'

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

    space

The following object is masked from 'package:S4Vectors':

    space

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

    lowess

Loading required package: plotrix

Attaching package: 'plotrix'

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

    plotCI

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/MAplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAplot
> ### Title: MAplotHelpfile
> ### Aliases: MAplot
> ### Keywords: DEGs MA MA plot
> 
> ### ** Examples
> 
> data(tRanslatomeSampleData)
> MAplot(limma.DEGs, outputformat="on screen",track="")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>