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Last data update: 2014.03.03

R: Selecting variables from result of MCIA

selectVar.mcia

R Documentation

Selecting variables from result of MCIA

Description

The selection of variables based on co-ordinates of MCIA variable space. The function is called by selectVar

Usage

## S3 method for class 'mcia'
selectVar(x, axis1 = 1, axis2 = 2, 
  a1.lim = c(-Inf, Inf), a2.lim = c(-Inf, Inf), 
  sepID.data = NULL, sepID.sep = "_", ...)

Arguments

`x`	An object of class `mcia`, the result returned by `mcia`.
`axis1`	Integer, the column number for the x-axis. The default is 1.
`axis2`	Integer, the column number for the y-axis. The default is 2.
`a1.lim`	The limited range of x-axis of selected. It could be either a vector (containing 2 numbers, the first value limiting the lower boundary, the second value limiting the upper boundary) or a list of vectors, each of which contains two number. If it is a `list`, the length of the `list` should be the same with number of `data.frame`s in `mcia`.
`a2.lim`	The limited range of y-axis.
`sepID.data`	See `plotVar.mcia`
`sepID.sep`	See `plotVar.mcia`
`...`	Other arguments

Details

mcia projecting variables (genes) from different datasets to a lower dimensional space. This function supplies a method selecting variables according to the co-ordinates of variables.

Value

Returns a data.frame describing which variables are presented on which data.frames within the limited region(s).

Author(s)

Chen Meng

Examples

  data(NCI60_4arrays)
  mcoin <- mcia(NCI60_4arrays)
  selectVar(mcoin, a1.lim=c(1, Inf))

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(omicade4)
Loading required package: ade4
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/omicade4/selectVar.mcia.Rd_%03d_medium.png", width=480, height=480)
> ### Name: selectVar.mcia
> ### Title: Selecting variables from result of MCIA
> ### Aliases: selectVar.mcia
> 
> ### ** Examples
> 
>   data(NCI60_4arrays)
>   mcoin <- mcia(NCI60_4arrays)
>   selectVar(mcoin, a1.lim=c(1, Inf))
         var agilent hgu133 hgu133p2 hgu95 stat
1    ST8SIA1    TRUE  FALSE    FALSE FALSE    1
2     S100A1    TRUE   TRUE    FALSE  TRUE    3
3      VEPH1    TRUE  FALSE    FALSE FALSE    1
4       CA14    TRUE  FALSE    FALSE FALSE    1
5      CD200    TRUE  FALSE    FALSE FALSE    1
6      MEF2C    TRUE  FALSE    FALSE FALSE    1
7    PCDHB16    TRUE  FALSE    FALSE FALSE    1
8  LOC729960    TRUE  FALSE    FALSE FALSE    1
9   C10orf90    TRUE  FALSE    FALSE FALSE    1
10     TRPM8    TRUE  FALSE    FALSE FALSE    1
11     S100B    TRUE   TRUE    FALSE FALSE    2
12   GPR137B   FALSE   TRUE    FALSE FALSE    1
13      CPN1   FALSE   TRUE    FALSE FALSE    1
14   FAM167B   FALSE   TRUE    FALSE  TRUE    2
15     ARNT2   FALSE   TRUE    FALSE FALSE    1
16  SERPINF1   FALSE   TRUE    FALSE FALSE    1
17    MAGEA5   FALSE   TRUE    FALSE FALSE    1
18      LPXN   FALSE   TRUE    FALSE FALSE    1
19     EDNRB   FALSE   TRUE    FALSE FALSE    1
20      NRP2   FALSE   TRUE    FALSE FALSE    1
21     GPNMB   FALSE   TRUE    FALSE FALSE    1
22  TNFRSF19   FALSE   TRUE    FALSE FALSE    1
23      GAS7   FALSE   TRUE    FALSE FALSE    1
24      LYST   FALSE   TRUE    FALSE FALSE    1
25     ADCY1   FALSE  FALSE     TRUE FALSE    1
26    ZNF697   FALSE  FALSE     TRUE FALSE    1
27    POU3F2   FALSE  FALSE     TRUE FALSE    1
28      QPCT   FALSE  FALSE     TRUE FALSE    1
29  C6orf218   FALSE  FALSE     TRUE FALSE    1
30     LAMA4   FALSE  FALSE     TRUE FALSE    1
31     CSPG4   FALSE  FALSE     TRUE FALSE    1
32     SPARC   FALSE  FALSE     TRUE FALSE    1
33    GAPDHS   FALSE  FALSE     TRUE FALSE    1
34    CITED1   FALSE  FALSE    FALSE  TRUE    1
35     TRPV2   FALSE  FALSE    FALSE  TRUE    1
36   MAGEA12   FALSE  FALSE    FALSE  TRUE    1
37      ACP5   FALSE  FALSE    FALSE  TRUE    1
38      PLP1   FALSE  FALSE    FALSE  TRUE    1
39     FABP7   FALSE  FALSE    FALSE  TRUE    1
40    MAGEA1   FALSE  FALSE    FALSE  TRUE    1
41    MAGEA3   FALSE  FALSE    FALSE  TRUE    1
42   MAGEA2B   FALSE  FALSE    FALSE  TRUE    1
43       TNC   FALSE  FALSE    FALSE  TRUE    1
44     SOX10   FALSE  FALSE    FALSE  TRUE    1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>