report {HTSanalyzeR} | R Documentation |
This is a generic function.
When implemented as the method of class GSCA
or NWA
,
this function produces reports for either the Gene Set Collection
Analysis or the Network Analysis.
To use report
for objects of class GSCA
or NWA
:
report(object, experimentName="Unknown", species=NULL, ntop=NULL, allSig=FALSE, keggGSCs=NULL, goGSCs=NULL, reportDir="HTSanalyzerReport")
report(object, ...)
object |
an object. When implemented as S4 methods of class |
... |
other arguments. (see below for the arguments supported by the method of
class |
a single character value specifying the name of the experiment (just for you own record)
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").
a single integer value specifying the number of plots to be produced for the GSEA results. For each gene set collection, plots are produced for the 'ntop' most significant gene sets.
a single logical value indicating 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 pValueCutoff
set in the function
analyze
. (see help(analyze)
for more details)
a character vector of names of all KEGG gene set collections. This will help create web links for KEGG terms.
a character vector of names of all GO gene set collections. This will help create web links for GO terms.
a single character value specifying the directory to store reports
This function take in the objects of the two wrapper classes (GSCA
and NWA
) and writes a report into the user-specified directory.
An index HTML file containing a summary of all results and hyperlinked
tabs 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 GSEA plots, enrichment maps and the 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 hyper-
geometric 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) ##report for a GSCA object data("KcViab_GSCA") ##append gene set terms to results KcViab_GSCA<-appendGSTerms(KcViab_GSCA, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF","GO_CC")) report(object=KcViab_GSCA, experimentName="KcViab", species="Dm", allSig=TRUE, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF","GO_CC"), reportDir="HTSanalyzerGSCAReport") browseURL(file.path(getwd(), "HTSanalyzerGSCAReport", "index.html")) ##report for a NWA object data("KcViab_NWA") report(object=KcViab_NWA, experimentName="KcViab", species="Dm", allSig=TRUE, keggGSCs="PW_KEGG", goGSCs=c("GO_BP","GO_MF","GO_CC"), reportDir="HTSanalyzerNWReport") browseURL(file.path(getwd(), "HTSanalyzerNWReport", "index.html")) ## End(Not run)