writeSigPathway

writeSP

a list containing the output from the
    <code>runSigPathway</code> function

spList

a data frame of top-ranked pathways from
    <code>rankPathways</code> or <code>rankPathways.NGSk</code>

rpDF

a list containing data frames of probes represented in
    gene sets from <code>getPathwayStatistics</code> or
    <code>getPathwayStatistics.NGSk</code>

gpsList

a list containing the values of parameters used
    in the analysis

parameterList

a character string specifying the file directory to
    write the results

resDir

a character string specifying the folder to write
    the results within <code>resDir</code>

outputDirName

a character string specifying the name for the
    HTML file containing the table of top-ranked pathways

topIndexFileName


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


htest

array

Conducts pathway analysis by calculating the NT_k and NE_k
statistics as described in Tian et al. (2005)

Weil Lai

sigPathway

Pathway Analysis

writeSigPathway function

a list containing the output from the
    <code>runSigPathway</code> function

a data frame of top-ranked pathways from
    <code>rankPathways</code> or <code>rankPathways.NGSk</code>

a list containing data frames of probes represented in
    gene sets from <code>getPathwayStatistics</code> or
    <code>getPathwayStatistics.NGSk</code>

a list containing the values of parameters used
    in the analysis

a character string specifying the file directory to
    write the results

a character string specifying the folder to write
    the results within <code>resDir</code>

a character string specifying the name for the
    HTML file containing the table of top-ranked pathways

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

writeSigPathway: Write results of pathway analysis to HTML format

Description

Usage

Arguments

Value

Details