Class "MetaArray" ~~~

Description

A class created for meta-analysis of microarray

Objects from the Class

Objects can be created by calls of the form new("MetaArray", ...).

Slots

GEDM:

Object of class "list" - gene expression data matrices are stored in individual slot of the list. Each matrix refer to one dataset, genes are represented in rows, samples in columns.

clinical:

Object of class "list" - clinical data matrices, clinical description of samples, rows refer to samples, columns to clinical characteristics

datanames:

Object of class "character" - vector of names of the datasets

Methods

plot

signature(x = "MetaArray", y = "missing"): draws distribution of clinical variables of several datasets. Boxplot is drawn for numerical variables and barplot for categorical ones.

print

signature(x = "MetaArray"): prints the number of samples and genes in each dataset, followed by summarization of each clinical characteristic of the samples

show

Same as print

as.list

Function transforms a MetaArray object into a list, in which each slot is again a list of three slots: gene expression data matrix GEDM, clinical data clinical, name of the dataset dataname

Author(s)

Ivana Ihnatova

Examples

showClass("MetaArray")

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(MAMA)
Loading required package: genefilter
Loading required package: metaMA

Attaching package: 'metaMA'

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

    rowVars

Loading required package: xtable
Loading required package: multtest
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

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: gtools
Loading required package: grid
Loading required package: GeneMeta

Attaching package: 'MAMA'

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

    multExpFDR, zScoreFDR, zScorePermuted, zScores

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MAMA/MetaArray.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MetaArray-class
> ### Title: Class "MetaArray" ~~~
> ### Aliases: MetaArray-class plot,MetaArray,missing-method
> ###   plot,MetaArray,ANY-method print,MetaArray-method
> ###   show,MetaArray-method as.list,MetaArray-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("MetaArray")
Class "MetaArray" [package "MAMA"]

Slots:
                                    
Name:       GEDM  clinical datanames
Class:      list      list character
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>