writeSigPathway {sigPathway} | R Documentation |
Writes the table of top-ranked pathways and their associated probe set to HTML files.
writeSigPathway(spList, resDir = getwd(), outputDirName = "sigPathway_results", topIndexFileName = "TopPathwaysTable.html") writeSP(rpDF, gpsList, parameterList = NULL, resDir = getwd(), outputDirName = "sigPathway_results", topIndexFileName = "TopPathwaysTable.html")
spList |
a list containing the output from the
runSigPathway function |
rpDF |
a data frame of top-ranked pathways from
rankPathways or rankPathways.NGSk |
gpsList |
a list containing data frames of probes represented in
gene sets from getPathwayStatistics or
getPathwayStatistics.NGSk |
parameterList |
a list containing the values of parameters used in the analysis |
resDir |
a character string specifying the file directory to write the results |
outputDirName |
a character string specifying the folder to write
the results within resDir |
topIndexFileName |
a character string specifying the name for the HTML file containing the table of top-ranked pathways |
These functions export the results of the pathway analysis (e.g.,
runSigPathway
) to several HTML files. The user can then
quickly browse through the files for genes of interest within the
top-ranked genes.
None returned
This function only uses the output of runSigPathway
to
generate the HTML files. Please see the help page of
runSigPathway
for example usage. The writeSP
function
should be used for those who have taken calculated the pathway
statistics separately as shown in the help file of calculate.NTk
,
calculate.NEk
, and calculate.NGSk
Weil Lai