epheno2html {phenoTest} | R Documentation |
Creates html files and plots using an epheno object, which stores the association between a list of variables and gene expression.
epheno2html(x, epheno, outputdir, prefix = "", genelimit = 50, categories = 3, withPlots = TRUE, mc.cores = 1)
x |
An object of class |
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. |
Evarist Planet
#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)