mergeGostatsResults: Merge enrichment results obtained for different databases...

Description Usage Arguments Details Value Author(s) See Also

View source: R/functions_enrich.R

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

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  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.

Value

NULL

Author(s)

Anne Biton

See Also

xtable, useMart, hyperGTest, GOHyperGParams, hypergeoAn, mergeGostatsResults


Bioconductor-mirror/MineICA documentation built on May 29, 2017, 8:30 a.m.