writeSigPathway: Write results of pathway analysis to HTML format

In sigPathway: Pathway Analysis

Description

Writes the table of top-ranked pathways and their associated probe set to HTML files.

Usage

writeSigPathway(spList, resDir = getwd(),
                outputDirName = "sigPathway_results",
                topIndexFileName = "TopPathwaysTable.html")
writeSP(rpDF, gpsList, parameterList = NULL, resDir = getwd(),
        outputDirName = "sigPathway_results",
        topIndexFileName = "TopPathwaysTable.html")

Arguments

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

Details

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.

Value

None returned

Note

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

Author(s)

Weil Lai

sigPathway documentation built on Nov. 8, 2020, 5:35 p.m.