Learn R Programming
sigPathway (version 1.40.0)

rankPathways.NGSk: 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

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.

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)

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