rankPathways.NGSk {sigPathway} | R Documentation

## Summarizes Top Pathways from One of the Pathway Analyses

### Description

Summarizes top pathways from one of the pathway analyses (i.e., `calculate.NTk`, `calculate.NEk`, `calculate.NGSk`, or `calculate.GSEA`)

### Usage

    rankPathways.NGSk(res.NGSk, G, gsList, methodName = "NGSk",
                      npath = 25)

### Arguments

`res.NGSk` | a list from the output of `calculate.NGSk`, `calculate.NTk`, `calculate.NEk`, or `calculate.GSEA`
`G` | a list containing the source, title, and probe sets associated with each curated pathway
`gsList` | a list containing three vectors from the output of the `selectGeneSets` function
`methodName` | a character vector of length 1 giving the name of the pathway analysis used in making `res.NGSk`
`npath` | an integer indicating the number of top gene sets to consider when ranking the top pathways

### Details

This function ranks the statistics given in `res.NGSk` and summarizes the top gene sets in a tabular format similar to Table 2 in Tian et al. (2005)

### Value

A data frame showing the pathways' indices in `G`, gene set category, pathway title, set size, `res.NGSk`'s statistics, the corresponding q-values, and the numerical ranks for the top gene sets.

### Note

See the help page for `calculate.NGSk` for example code that uses `rankPathways.NGSk`

### Author(s)

Lu Tian, Peter Park, and Weil Lai

### References

Tian L., Greenberg S.A., Kong S.W., Altschuler J., Kohane I.S., Park P.J. (2005) Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences of the USA, 102, 13544-9.

http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102

[Package sigPathway version 1.12.1 Index]