writeGostatsHtmltable {MineICA} | R Documentation

## Writes enrichment results in a HTML file

### Description

This function takes as input in argument `d` the output of function `addGenesToGoReport` whose goal is to add genes included in gene sets detected as significantly enriched by `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.

### Usage

      writeGostatsHtmltable(d, label, side = "both", db, file,
        cutoff = 3)

### Arguments

`d` | A data.frame describing enrichment results, output of function `hyperGTest`
`label` | The label of the data the results originate from
`side` | The side of the component used for enrichment analysis
`db` | The database used ("GO" or "KEGG")
`file` | File name for output
`cutoff` | The threshold used to select the genes used to run the enrichment analysis

### Value

NULL

### Author(s)

Anne Biton

### See Also

`xtable`, `addGenesToGoReport`, `hyperGTest`

### 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")

[Package MineICA version 1.28.0 Index]