'GLA' is used to calculate the GLA estimate for a gene triplet data.
Arguments
object
An numerical matrix object with three columns or an object of ExpresionSet class with three features.
cut
cut==M +1. M is the number of grip points pre-specifed over the third variable.
dim
An index of the column for the gene to be treated as the third controller variable. Default is dim=3
geneMap
A character vector with three elements representing the mapping between gene names and feature names (optional).
Details
The input object can be a numerical matrix with three columns with row representing observations and column representing three variables. It can also be an ExpressionSet object with three features. If input a matrix class data, all three columns of the object representing the variables should have column names. Each variable in the object will be standardized with mean 0 and variance 1 in the function. In addition, the third variable will be quantile normalized within the function. More detail example about the usage of geneMap is demonstrated in the vignette.
Value
'GLA' returns a numerical value representing the estimated value. A more detailed interpretation of the value is illustrated in the vignette.
Author(s)
Yen-Yi Ho
References
Yen-Yi Ho, Leslie Cope, Thomas A. Louis, and Giovanni Parmigiani, GENERALIZED LIQUID ASSOCIATION (April 2009). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper
183. http://www.bepress.com/jhubiostat/paper183
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> library(LiquidAssociation)
Loading required package: geepack
Loading required package: yeastCC
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: org.Sc.sgd.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LiquidAssociation/GLA-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GLA-methods
> ### Title: Function to calculate GLA estimate
> ### Aliases: GLA-methods GLA,eSet-method GLA,matrix-method GLA
> ### Keywords: methods
>
> ### ** Examples
>
>
> data<-matrix(rnorm(300), ncol=3)
>
> colnames(data)<-c("Gene1", "Gene2", "Gene3")
>
> GLAest<-GLA(data, cut=4, dim=3)
>
> GLAest
GLA(Gene1,Gene2|Gene3)
-0.05445531
>
>
>
>
>
>
> dev.off()
null device
1
>