Liquid Associaiton Package

Description

The LiquidAssociation package provide methods to examine a special kind of three-way interaction called liquid association. The term liquid association was first proposed by contains functions for calculate direct and model-based estimators for liquid associaiton. It also provides functions for testing the existence of liquid associaiton given a gene triplet data.

Details

GLA LA CNM.full CNM.simple getsGLA getsLA plotGLA

Author(s)

Yen-Yi Ho <yho@jhsph.edu>

Maintainer: Yen-Yi Ho <yho@jhsph.edu>

References

Ker-Chau Li, Genome-wide coexpression dynamics: theory and application (2002). PNAS 99 (26): 16875-16880.

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

Examples

data<-matrix(rnorm(300), ncol=3)

colnames(data)<-c("Gene1", "Gene2", "Gene3")

FitCNM.full<-CNM.full(data)

FitCNM.full

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 '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
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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/LiquidAssociation-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LiquidAssociation-package
> ### Title: Liquid Associaiton Package
> ### Aliases: LiquidAssociation-package LiquidAssociation
> ### Keywords: package
> 
> ### ** Examples
> 
> data<-matrix(rnorm(300), ncol=3)
> 
> colnames(data)<-c("Gene1", "Gene2", "Gene3")
> 
> FitCNM.full<-CNM.full(data)
> 
> FitCNM.full
Model: CNM(Gene1,Gene2|Gene3)
     estimates     san.se        wald   p value
a3 -0.02366585 0.12469808 0.036018414 0.8494775
a4 -0.01405887 0.14982217 0.008805385 0.9252386
a5  0.09046321 0.20449493 0.195694612 0.6582187
b1 -0.06918418 0.10533409 0.431395603 0.5113049
b2 -0.03824931 0.09698809 0.155528626 0.6933070
b3 -0.17965260 0.12858622 1.951992477 0.1623723
b4  0.06592465 0.12362790 0.284356124 0.5938602
b5  0.03647130 0.21636024 0.028415001 0.8661368
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>