writeGostatsHtmltable: Writes enrichment results in a HTML file

Description Usage Arguments Value Author(s) See Also Examples

View source: R/functions_enrich.R

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

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  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

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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")

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