writeGostatsHtmltable: Writes enrichment results in a HTML file

In MineICA: Analysis of an ICA decomposition obtained on genomics data

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")

MineICA documentation built on Nov. 8, 2020, 5:35 p.m.