Rのヘルプ機能

"made4"というパッケージをインストールするとします。

source("http://www.bioconductor.org/biocLite.R")
biocLite("made4")

"made4"とういうパッケージについて知りたいときは次のコマンドを入力します。

help(package = "made4")

すると・・・、


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html3D                  Produce web page with a 3D graph that can be
                        viewed using Chime web browser plug-in, and/or
                        a pdb file that can be viewed using Rasmol
khan                    Microarray gene expression dataset from Khan et
                        al., 2001. Subset of 306 genes.
ord                     Ordination
overview                Draw boxplot, histogram and hierarchical tree
                        of gene expression data
plotarrays              Graph xy plot of variable (array) projections
                        from ordination, between group analysis or
                        coinertia analysis.
plotgenes               Graph xy plot of variable (gene) projections
                        from PCA or COA. Only label variables at ends
                        of axes
pretty.dend             Draw hierarchical tree of gene expression data
                        with a colorbar for numerous class vectors
randomiser              Randomly reassign training and test samples
sumstats                Summary statistics on xy co-ordinates, returns
                        the slopes and distance from origin of each
                        co-ordinate.
suppl                   Projection of supplementary data onto axes from
                        a between group analysis
topgenes                Topgenes, returns a list of variables at the
                        ends (positive, negative or both) of an axis

これ以上の情報はディレクトリ
'/home/kappa/R/i486-pc-linux-gnu-library/2.10/made4/doc'
にある以下のビニエット中にあります：

introduction: Made4 An Introduction (HowTo) (source, pdf)

(END)

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のようにヘルプが表示されます。この中にあるtopgenesという関数の使用方法を知りたいとします。すると

まず、"q"で現在の表示を閉じてコマンド入力モードにしたあと

help(topgenes)

で下が表示されます

----------------------------------------

topgenes                 package:made4                 R Documentation

Topgenes, returns a list of variables at the ends (positive, negative
or both) of an axis

Description:

     ‘topgenes’ will return a list of the top N variables from the
     positive, negative or both ends of an axis. That is, it returns a
     list of variables that have the maximum and/or minimum values in a
     vector.

Usage:

     topgenes(x, n = 10, axis = 1, labels = row.names(x), ends = "both", ...)
    
Arguments:

       x: A ‘vector’, ‘matrix’ or ‘data.frame’. Typically a data
          frame \$co or \$li from ‘dudi’ or \$ls, \$li, \$co from
          ‘bga’.

       n: An integer indicating the number of variables to be returned.
          Default is 5.

    axis: An integer indicating the column of x. Default is 1 (first
          axis, of \$co or \$li file)

  labels: A vector of row names, for x[,axis]. Default values is
          row.names(x)

:

--------------------------------

さらには、サンプルプログラムを実行したいときは

 example(topgenes)

とすれば、topgenes関数を用いた解析コマンドが表示されます。