Visualise for each gene the condition-specific detection result from SpeCond

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Description

getGeneHtmlPage generates html results pages for a set of genes as well as an index page. The index allows to navigate between the gene result pages.

Usage

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getGeneHtmlPage(expressionMatrix, specificResult, 
name.index.html = "index.html", prefix.file = NULL, 
outdir="Single_result_pages", gene.html = NULL, 
gene.html.ids = c(1:10))

Arguments

expressionMatrix

the matrix of expression values initially used

specificResult

the sp_list class object result of the getSpecificProbeset function

name.index.html

the name of the html index, by default is index.html

prefix.file

a prefix added to the generated file(s) and outdir directory name to linked to the index file. The default is NULL, the prefix.file attribute of specificResult is used

outdir

the name of the directory in which the generated files will be created. The default is "Single_result_pages"

gene.html

a vector of gene names for which you want to create html pages, same as the row names of the expressionMatrix object. The default is NULL (the values of the gene.html.ids argument will be used)

gene.html.ids

a vector of integer corresponding to the row numbers in the expressionMatrix object of the genes for which you want to create html pages. The default is the 10 first rows (or the number of row of the expressionMatrix if inferior to 10)

Details

The main file name.index.html is created in the current directory. The result page(s) to which it points are created in the outdir directory. If both gene.html and gene.html.ids are set to NULL, the gene html pages for every gene in the expressionMatrix object will be generated It is useful to change the prefix when you create a new index as well as changing the name.index.html value. As you may want to get index with the same genes but different parameters set and plots so using a different specificResult object. It is possible to use gene.html or gene.html.ids to select a list of gene.

Author(s)

Florence Cavalli, florence@ebi.ac.uk

See Also

getFullHtmlSpeCondResult

Examples

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library(SpeCond)
data(expressionSpeCondExample)
##Perform the condition specific detection analysis with SpeCond()
generalResult=SpeCond(expressionSpeCondExample, param.detection=NULL,
 multitest.correction.method="BY", prefix.file="E", print.hist.pv=TRUE, fit1=NULL, 
 fit2=NULL, specificOutlierStep1=NULL)
specificResult=generalResult$specificResult
##Produce the Gene html page results for the first 20 genes using the specificResult 
##object
genePageInfo=getGeneHtmlPage(expressionSpeCondExample, specificResult, 
 name.index.html="index_example_SpeCond_Results.html", outdir=
 "Single_result_pages_dir", gene.html.ids=c(1:20))