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Last data update: 2014.03.03

R: Selecting variables (genes) from result of MCIA or CIA...

selectVar

R Documentation

Selecting variables (genes) from result of MCIA or CIA according to co-ordinates

Description

The user level function calls selectVar.mcia or selectVar.cia. Function cia or mcia projects variables (genes) from different datasets to a 2 dimensional space. This function supplies a method selecting variables (genes) according to the coordinates of variables

Usage

  selectVar(x, axis1 = 1, axis2 = 2, ...)

Arguments

`x`	An object of class `cia` or `mcia`, the result returned by `cia` or `mcia` respectively.
`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.
`...`	Other arguments

Value

Returns a data.frame describing which variables (genes) 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(2, Inf), a2.lim=c(-Inf, Inf))

# an example for the usage of sepID.data and sepID.sep
nci60_mod <- NCI60_4arrays
rownames(nci60_mod$hgu95) <- paste(rownames(nci60_mod$hgu95), "s1", sep="_")
mcoin_mod <- mcia(nci60_mod)
# without specifing
selectVar(mcoin_mod, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf))
# specifing the sepID.data and sepID.sep
selectVar(mcoin_mod, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf), sepID.data=4, sepID.sep="_")

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(omicade4)
Loading required package: ade4
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/omicade4/selectVar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: selectVar
> ### Title: Selecting variables (genes) from result of MCIA or CIA according
> ###   to co-ordinates
> ### Aliases: selectVar
> 
> ### ** Examples
> 
> 
> data(NCI60_4arrays)
> mcoin <- mcia(NCI60_4arrays)
> selectVar(mcoin, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf))
       var agilent hgu133 hgu133p2 hgu95 stat
1  ST8SIA1    TRUE  FALSE    FALSE FALSE    1
2   S100A1    TRUE   TRUE    FALSE  TRUE    3
3 C10orf90    TRUE  FALSE    FALSE FALSE    1
4    S100B    TRUE   TRUE    FALSE FALSE    2
5    GPNMB   FALSE   TRUE    FALSE FALSE    1
6 C6orf218   FALSE  FALSE     TRUE FALSE    1
7     ACP5   FALSE  FALSE    FALSE  TRUE    1
8     PLP1   FALSE  FALSE    FALSE  TRUE    1
9    SOX10   FALSE  FALSE    FALSE  TRUE    1
> 
> # an example for the usage of sepID.data and sepID.sep
> nci60_mod <- NCI60_4arrays
> rownames(nci60_mod$hgu95) <- paste(rownames(nci60_mod$hgu95), "s1", sep="_")
> mcoin_mod <- mcia(nci60_mod)
> # without specifing
> selectVar(mcoin_mod, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf))
         var agilent hgu133 hgu133p2 hgu95 stat
1    ST8SIA1    TRUE  FALSE    FALSE FALSE    1
2     S100A1    TRUE   TRUE    FALSE FALSE    2
3   C10orf90    TRUE  FALSE    FALSE FALSE    1
4      S100B    TRUE   TRUE    FALSE FALSE    2
5      GPNMB   FALSE   TRUE    FALSE FALSE    1
6   C6orf218   FALSE  FALSE     TRUE FALSE    1
7    ACP5_s1   FALSE  FALSE    FALSE  TRUE    1
8    PLP1_s1   FALSE  FALSE    FALSE  TRUE    1
9  S100A1_s1   FALSE  FALSE    FALSE  TRUE    1
10  SOX10_s1   FALSE  FALSE    FALSE  TRUE    1
> # specifing the sepID.data and sepID.sep
> selectVar(mcoin_mod, a1.lim=c(2, Inf), a2.lim=c(-Inf, Inf), sepID.data=4, sepID.sep="_")
       var agilent hgu133 hgu133p2 hgu95 stat
1  ST8SIA1    TRUE  FALSE    FALSE FALSE    1
2   S100A1    TRUE   TRUE    FALSE  TRUE    3
3 C10orf90    TRUE  FALSE    FALSE FALSE    1
4    S100B    TRUE   TRUE    FALSE FALSE    2
5    GPNMB   FALSE   TRUE    FALSE FALSE    1
6 C6orf218   FALSE  FALSE     TRUE FALSE    1
7     ACP5   FALSE  FALSE    FALSE  TRUE    1
8     PLP1   FALSE  FALSE    FALSE  TRUE    1
9    SOX10   FALSE  FALSE    FALSE  TRUE    1
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>