mergeGostatsResults: Merge enrichment results obtained for different databases into one file per component.
Description
This function is internal and called by function
runEnrich. It merges enrichment results obtained
with either KEGG, GO, or both databases into one file.
Usage
mergeGostatsResults(resPath, GOstatsPath, rdata = "hgres", cutoffs = NULL, hgCutoff = 0.01, cond = TRUE, pathGenes)
Arguments
resPath
The global path where results of ICA
analysis are written
GOstatsPath
The path within argument
resPath where files will be written
rdata
The name of the rdata file containing the
enrichment analysis of all components
cutoffs
The threshold(s) used to select genes used
in enrichment analysis
hgCutoff
The p-value threshold
cond
A logical indicating whether the calculation
has been conditioned on the GO structure, see
GOHyperGParams. pathGenes
The path where HTML files containing
gene projections for each component are located
Details
This function writes an HTML file per component,
containing the outputs of the enrichment tests computed
through the function hyperGTest.
The results of the enrichment tests are loaded from .rda
files located in
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
resPath(icaSet)/zvalCutoff(params). The
arguments hgCutoff and 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 hyperGTest that
are given in each table are:
- DB, ID,
Term
- The database, the gene set ID, and the gene set
name,
- 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
, - Expected counts
- expected
number of genes in the selected gene list to be found at
each tested category term/gene set,
- 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,
- Counts
- number
of genes in the selected gene list which are annotated
for the gene set,
- Size
- number of genes from the
universe annotated for the gene set.