This function is internal and called by function
runEnrich. It merges enrichment results obtained
with either KEGG, GO, or both databases into one file.
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The global path where results of ICA analysis are written
The path within argument
The name of the rdata file containing the enrichment analysis of all components
The threshold(s) used to select genes used in enrichment analysis
The p-value threshold
A logical indicating whether the calculation
has been conditioned on the GO structure, see
The path where HTML files containing gene projections for each component are located
This function writes an HTML file per component,
containing the outputs of the enrichment tests computed
through the function
The results of the enrichment tests are loaded from .rda
files located in
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
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.
The outputs of
are given in each table are:
The database, the gene set ID, and the gene set name,
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
expected number of genes in the selected gene list to be found at each tested category term/gene set,
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,
number of genes in the selected gene list which are annotated for the gene set,
number of genes from the universe annotated for the gene set.
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