writeSigPathway {sigPathway} | R Documentation

## Write results of pathway analysis to HTML format

### 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

[Package sigPathway version 1.12.1 Index]