rankPathways.NGSk: Summarizes Top Pathways from One of the Pathway Analyses
In sigPathway: Pathway Analysis

Description Usage Arguments Details Value Note Author(s) References

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

1 2	rankPathways.NGSk(res.NGSk, G, gsList, methodName = "NGSk", npath = 25)

`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

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)

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.

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

Lu Tian, Peter Park, and Weil Lai

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

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