writeReportHTSA {HTSanalyzeR} | R Documentation |
This function writes an HTML report following a complete analysis
of a data set with the objects of class GSCA
and/or NWA
.
writeReportHTSA(gsca, nwa, experimentName="Unknown", species=NULL, ntop=NULL, allSig=FALSE, keggGSCs=NULL, goGSCs=NULL, reportDir= "HTSanalyzerReport")
gsca |
an object of class |
nwa |
an object of class |
experimentName |
a single character value specifying the name of the experiment (just for you own record) |
species |
a single character value specifying the species for which the data should be read. The current version supports one of the following species: "Dm" ("Drosophila_melanogaster"), "Hs" ("Homo_sapiens"), "Rn" ("Rattus_ norvegicus"), "Mm" ("Mus_musculus"), "Ce" ("Caenorhabditis_elegans"). |
ntop |
a single integer value specifying the number of plots to be produced for the GSEA analysis. For each gene set collection, plots are produced for the 'ntop' most significant gene sets. |
allSig |
a single logical value determining whether or not to generate plots for
all significant gene sets. A gene set is significant if its corresponding
adjusted p-value is less than the |
keggGSCs |
a character vector of the names of all KEGG gene set collections. This will help create web links for KEGG terms. |
goGSCs |
a character vector of the names of all GO gene set collections. This will help create web links for GO terms. |
reportDir |
a single character value specifying the directory to store reports |
This function takes in the objects of the two wrapper classes (GSCA
and NWA
) and writes a report into a user-specified directory.
An index HTML file containing a summary of all results and hyperlinked tabs
linking to more detailed results will be generated in the root directory.
The other HTML files will be stored in a subdirectory called 'html'. All
images including the GSEA plots, enrichment maps and subnetwork figure will
be produced in a subdirectory called 'image'. All documents or text files
such as the files containing significant gene sets of the hypergeometric
test results will be stored in a subdirectory called 'doc'.
Xin Wang, Camille Terfve
## Not run: ##(see the vignette for details about the preprocessing of this data set) library(KEGG.db) library(GO.db) library(AnnotationDbi) data("KcViab_GSCA") data("KcViab_NWA") ##append gene set terms to results KcViab_GSCA<-appendGSTerms(KcViab_GSCA, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF","GO_CC")) ##report both analyses writeReportHTSA(gsca=KcViab_GSCA, nwa=KcViab_NWA, experimentName="KcViab", species="Dm", allSig=TRUE, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF", "GO_CC"), reportDir="HTSanalyzerReport") browseURL(file.path(getwd(), "HTSanalyzerReport", "index.html")) ## End(Not run)