View source: R/functions_enrich.R
writeGostatsHtmltable | R Documentation |
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.
writeGostatsHtmltable(d, label, side = "both", db, file,
cutoff = 3)
d |
A data.frame describing enrichment results,
output of function |
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 |
NULL
Anne Biton
xtable
,
addGenesToGoReport
,
hyperGTest
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")
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