R: Save HTML file with global gene scores from functional gene...
activeModScoreHTML
R Documentation
Save HTML file with global gene scores from functional gene
groups classification
Description
This function takes an object of class maigesActMod,
that is generated using the function activeMod to do
functional classification of gene groups, and save an HTML file with
global score for genes separated by gene groups (modules).
## Loading a little dataset
data(gastro)
## Doing functional classification of gene groups for 'Tissue' sample label
gastro.mod = activeMod(gastro.summ, sLabelID="Tissue", cutExp=1,
cutPhiper=0.05)
activeModScoreHTML(gastro.mod)
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/activeModScoreHTML.Rd_%03d_medium.png", width=480, height=480)
> ### Name: activeModScoreHTML
> ### Title: Save HTML file with global gene scores from functional gene
> ### groups classification
> ### Aliases: activeModScoreHTML
> ### Keywords: methods
>
> ### ** Examples
>
> ## Loading a little dataset
> data(gastro)
>
> ## Doing functional classification of gene groups for 'Tissue' sample label
> gastro.mod = activeMod(gastro.summ, sLabelID="Tissue", cutExp=1,
+ cutPhiper=0.05)
>
> activeModScoreHTML(gastro.mod)
>
>
>
>
>
> dev.off()
null device
1
>