epheno2html {phenoTest} | R Documentation

## Create html files and plots from an epheno object.

### Description

Creates html files and plots using an epheno object, which stores the association between a list of variables and gene expression.

### Usage

    epheno2html(x, epheno, outputdir, prefix = "", genelimit = 50, categories = 3, withPlots = TRUE, mc.cores = 1)

### Arguments

`x` | An object of class `ExpressionSet` (used to generate the epheno object) containing expression levels in exprs(x), phenotype information in pData(x) and annotation in annotation(x).
`epheno` | an object produced by ExpressionPhenoTest. this object will contain univariate association between a list of phenotype variables and gene expression as weel as p-values.
`outputdir` | where to place files.
`prefix` | will be used to add a text to the beginning of the files that will be created.
`genelimit` | maximum number of genes on the list.
`categories` | Number of categories used for continuous variables. It has to be the same as the one used for ExpressionPhenoTest.
`withPlots` | when FALSE no plots will be produced. Makes the process faster.
`mc.cores` | number of cores that will be used to run the process.

### Author(s)

Evarist Planet

### Examples

    #Example on building homology tables for human.
    #mart <- useMart("ensembl", "hsapiens_gene_ensembl")
    #homol.symbol <- getLDS(attributes = c("entrezgene"),
    #    mart = mart, attributesL = c("external_gene_id"),
    #    martL = mart, filters = "entrezgene", values = entrezid)
    #mart <- useMart("ensembl", "hsapiens_gene_ensembl")
    #homol.genename <- getLDS(attributes = c("entrezgene"),
    #    mart = mart, attributesL = c("description"), martL = mart,
    #    filters = "entrezgene", values = entrezid)

[Package phenoTest version 1.35.1 Index]