Save HTML file with scores and p-values from functional gene networks classification

Description

This function takes an object of class maigesActNet, that is generated using the function activeNet to do functional classification of gene groups, and save an HTML file with global score for genes separated by gene groups (modules).

Usage

activeNetScoreHTML(mod=NULL, dir="./", fileSave="scores")

Arguments

Value

This function generates an HTML file and don't return any R value or object.

Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

See Also

plot.maigesActNet, activeNet

Examples

## Loading the dataset
data(gastro)

## Doing functional classification of gene networks for sample Label
## given by 'Tissue'
gastro.net = activeNet(gastro.summ, sLabelID="Tissue")

activeNetScoreHTML(gastro.net)

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(maigesPack)
Loading required package: convert
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: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: marray
Loading required package: graph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maigesPack/activeNetScoreHTML.Rd_%03d_medium.png", width=480, height=480)
> ### Name: activeNetScoreHTML
> ### Title: Save HTML file with scores and p-values from functional gene
> ###   networks classification
> ### Aliases: activeNetScoreHTML
> ### Keywords: methods
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Doing functional classification of gene networks for sample Label
> ## given by 'Tissue'
> gastro.net = activeNet(gastro.summ, sLabelID="Tissue")
> 
> activeNetScoreHTML(gastro.net)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>