epheno2html: Create html files and plots from an epheno object.

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

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)

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.