new file mode 100644

@@ -0,0 +1,61 @@

+\name{writeGostatsHtmltable}

+\alias{writeGostatsHtmltable}

+\title{Writes enrichment results in a HTML file}

+\usage{

+  writeGostatsHtmltable(d, label, side = "both", db, file,

+    cutoff = 3)

+}

+\arguments{

+  \item{d}{A data.frame describing enrichment results,

+  output of function \code{\link[Category]{hyperGTest}}}

+

+  \item{label}{The label of the data the results originate

+  from}

+

+  \item{side}{The side of the component used for enrichment

+  analysis}

+

+  \item{db}{The database used ("GO" or "KEGG")}

+

+  \item{file}{File name for output}

+

+  \item{cutoff}{The threshold used to select the genes used

+  to run the enrichment analysis}

+}

+\value{

+  NULL

+}

+\description{

+  This function takes as input in argument \code{d} the

+  output of function \code{\link{addGenesToGoReport}} whose

+  goal is to add genes included in gene sets detected as

+  significantly enriched by

+  \code{\link[Category]{hyperGTest}} function. It writes

+  the enrichment results in an HTML file which redirects

+  each gene set ID to its web-description and each gene to

+  its Gene Card web-page.

+}

+\examples{

+hgOver <- structure(list(GOBPID = c("GO:0003012", "GO:0030049"),

+                    Pvalue = c(1.70848789161935e-10, 6.62508415367712e-05),

+                    OddsRatio = c(22.1043956043956, 26.4190476190476),

+                    ExpCount = c(1.19549929676512, 0.246132208157525),

+                    Count = c(12L, 4L), Size = c(68L, 14L),

+                    Term = c("muscle system process", "muscle filament sliding"),

+                    In_geneSymbols = c("ACTA2,ACTC1,ACTG2,CASQ2,CNN1,DES,MYH3,MYLK,PTGS1,TPM2,MYL9,LMOD1","ACTC1,DES,MYH3,TPM2")),

+                    .Names = c("GOBPID", "Pvalue", "OddsRatio", "ExpCount", "Count", "Size", "Term", "In_geneSymbols"),

+                    class = "data.frame", row.names=1:2)

+

+MineICA:::writeGostatsHtmltable(d=hgOver, label="Example of enrichment analysis", db="KEGG",

+                                file="outputHyper_example.htm")

+}

+\author{

+  Anne Biton

+}

+\seealso{

+  \code{\link[xtable]{xtable}},

+  \code{\link{addGenesToGoReport}},

+  \code{\link[Category]{hyperGTest}}

+}

+\keyword{internal}

+