phenoTest (version 1.20.0)

epheno2html: 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.

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)