R: Selecting top weighted variables (genes) from result of MCIA...
topVar
R Documentation
Selecting top weighted variables (genes) from result of MCIA or CIA
Description
The user level function calls topVar.mcia or
topVar.cia. This function provides a method selecting
top weighted variables (genes) on an axis (either positive side or negative side or both).
Usage
topVar(x, axis = 1, end = "both", topN = 5)
Arguments
x
an object of class mcia or cia
axis
an interger to sepecify which axis to check
end
which end of the axis to check, could be positive,
negative or both. Any unambiguous substring can be given.
topN
An integer. The number of top weighted variable to return.
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/topVar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: topVar
> ### Title: Selecting top weighted variables (genes) from result of MCIA or
> ### CIA
> ### Aliases: topVar
>
> ### ** Examples
>
> data(NCI60_4arrays)
> mcoin <- mcia(NCI60_4arrays)
> topVar(mcoin, axis = 1, end = "both", topN = 3)
ax1_agilent_positive ax1_agilent_negative ax1_hgu133_positive
1 S100B.agilent SCNN1A.agilent GPNMB.hgu133
2 ST8SIA1.agilent FAM83B.agilent S100B.hgu133
3 C10orf90.agilent NSUN7.agilent S100A1.hgu133
ax1_hgu133_negative ax1_hgu133p2_positive ax1_hgu133p2_negative
1 GSTO2.hgu133 C6orf218.hgu133p2 TSPAN8.hgu133p2
2 EGFR.hgu133 CSPG4.hgu133p2 DSP.hgu133p2
3 AREG.hgu133 POU3F2.hgu133p2 LAMA3.hgu133p2
ax1_hgu95_positive ax1_hgu95_negative
1 PLP1.hgu95 IGFBP4.hgu95
2 SOX10.hgu95 S100A14.hgu95
3 ACP5.hgu95 FERMT1.hgu95
>
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>
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> dev.off()
null device
1
>