Sets of items and their annotations

Description

This class describes sets, items and their annotations.

Details

Internally, the method mgsa indexes all elements of the sets before fitting the model. In case mgsa must be run on several observations with the same gene sets, computations can be speeded up by performing this indexing once for all. This can be achieved by building a MgsaSets. In order to ensure consistency of the indexing, no replace method for any slot is provided. Accessors are available.

The data frames setAnnotations and itemAnnotations allow to store annotations. No constraint is imposed on the number and names of their columns.

Slots

sets

A list whose elements are vector of item indices.

itemName2ItemIndex

The mapping of item names to index.

numberOfItems

How many items?

setAnnotations

Annotations of the sets. The rownames are set names.

itemAnnotations

Annotations of the items. The rownames are item names.

See Also

MgsaGoSets, readGAF, mgsa

Examples

new("MgsaSets", sets=list(set1=c("a", "b"), set2=c("b", "c")))

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(mgsa)
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mgsa/MgsaSets-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MgsaSets-class
> ### Title: Sets of items and their annotations
> ### Aliases: MgsaSets-class
> 
> ### ** Examples
> 
> new("MgsaSets", sets=list(set1=c("a", "b"), set2=c("b", "c")))
Object of class MgsaSets
2 sets over 3 unique items.

Set annotations:
data frame with 0 columns and 2 rows

Item annotations:
data frame with 0 columns and 3 rows
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>