Generalized log transformation function

Description

This function transforms the input values by the generalized log function.

Usage

glog(y, lambda)

Arguments

Details

The glog transformation of a variable y is defined as log(y + sqrt(y^2 + lambda)). Using lambda = 0 corresponds to the log transformation, up to a scale factor of 2. (Other, equivalent expressions exist for the glog transformation. See Durbin et al. (2002) and Huber et al. (2002) for futher details.)

The input matrix y may be modified prior to transformation by subtracting a constant or vector ("alpha"). The parameters lambda and alpha may be estimated from tranest.

Value

Author(s)

David Rocke and Geun-Cheol Lee

References

Durbin, B.P., Hardin, J.S., Hawkins, D.M., and Rocke, D.M. (2002) A variance-stabilizing transformation for gene-expression microarray data, Bioinformatics, 18, S105–S110.

Huber, W., Von Heydebreck, A., Sueltmann, H., Poustka, A., and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics, 18, S96–S104.

http://dmrocke.ucdavis.edu

See Also

tranest, transeS

Examples

#library
library(Biobase)
library(LMGene)

#data
data(sample.mat)
sample.mat[1:5,1:4]

GloggedSmpd<-glog(sample.mat-50,500)
GloggedSmpd[1:5,1:4]

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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'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(LMGene)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: multtest
Loading required package: survival
Loading required package: affy

Attaching package: 'LMGene'

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

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LMGene/glog.Rd_%03d_medium.png", width=480, height=480)
> ### Name: glog
> ### Title: Generalized log transformation function
> ### Aliases: glog
> ### Keywords: math
> 
> ### ** Examples
> 
> #library
> library(Biobase)
> library(LMGene)
> 
> #data
> data(sample.mat)
> sample.mat[1:5,1:4]
   p1d0 p1d1 p1d2 p1d3
g1  216  149  169  113
g2  334  311  187  135
g3  398  367  351  239
g4  691  614  401  251
g5  568  452  370  247
> 
> GloggedSmpd<-glog(sample.mat-50,500)
> GloggedSmpd[1:5,1:4]
       p1d0     p1d1     p1d2     p1d3
g1 5.809641 5.300784 5.480983 4.866384
g2 6.343668 6.259498 5.619722 5.152667
g3 6.546380 6.453291 6.401634 5.938375
g4 7.156481 7.028594 6.554946 5.999532
g5 6.943588 6.690372 6.462687 5.979556
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>