MetaArray: Class "MetaArray" ~~~

In MAMA: Meta-Analysis of MicroArray

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")

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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

Class "MetaArray" [package "MAMA"]

Slots:
                                    
Name:       GEDM  clinical datanames
Class:      list      list character

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.