\name{mergeGostatsResults}
\alias{mergeGostatsResults}
\title{Merge enrichment results obtained for different databases into one file per component.}
\usage{
mergeGostatsResults(resPath, GOstatsPath,
rdata = "hgres", cutoffs = NULL, hgCutoff = 0.01,
cond = TRUE, pathGenes)
}
\arguments{
\item{resPath}{The global path where results of ICA
analysis are written}

\item{GOstatsPath}{The path within argument
\code{resPath} where files will be written}

\item{rdata}{The name of the rdata file containing the
enrichment analysis of all components}

\item{cutoffs}{The threshold(s) used to select genes used
in enrichment analysis}

\item{hgCutoff}{The p-value threshold}

\item{cond}{A logical indicating whether the calculation
has been conditioned on the GO structure, see

\item{pathGenes}{The path where HTML files containing
gene projections for each component are located}
}
\value{
NULL
}
\description{
This function is internal and called by function
\code{runEnrich}. It merges enrichment results obtained
with either KEGG, GO, or both databases into one file.
}
\details{
This function writes an HTML file per component,
containing the outputs of the enrichment tests computed
The results of the enrichment tests are loaded from .rda
files located in
\code{resPath(icaSet)}/GOstatsEnrichAnalysis/byDb/'db-name'/('ontology-name'/).
The results obtained for the different
databases/ontologies are then merged into an array for
each component, this array is written as an HTML file in
the directory
\code{resPath(icaSet)}/\code{zvalCutoff(params)}. The
arguments \code{hgCutoff} and \code{cond} have to be
provided because they will be used in the file names of
the resulting files.

This function makes several important assumptions: only
databases GO and KEGG have been tested, p-values are not
available for gene sets that have not been selected as
significant.

are given in each table are: \describe{ \item{DB, ID,
Term}{The database, the gene set ID, and the gene set
name,} \item{P-value}{probability of observing the number
of genes annotated for the gene set among the selected
gene list, knowing the total number of annotated genes
among the universe}, \item{Expected counts}{expected
number of genes in the selected gene list to be found at
each tested category term/gene set,} \item{Odds
ratio}{odds ratio for each category term tested which is
an indicator of the level of enrichment of genes within
the list as against the universe,} \item{Counts}{number
of genes in the selected gene list which are annotated
for the gene set,} \item{Size}{number of genes from the
universe annotated for the gene set.}}
}
\author{
Anne Biton
}
\seealso{