rankPathways {sigPathway}R Documentation

Summarizes Top Pathways from Pathway Analyses

Description

Summarizes top pathways from pathway analyses.

Usage

rankPathways(res.A, res.B, G, gsList, methodNames = NULL, npath = 25)

Arguments

res.A a list from the output of calculate.NTk or calculate.NEk
res.B a list from the output of calculate.NTk or calculate.NEk
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
methodNames a character vector of length 2 giving the names for res.A and res.B
npath an integer indicating the number of top gene sets to consider from each statistic when ranking the top pathways

Details

This function ranks together the statistics given in res.A and res.B 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.A's statistics, res.B's statistics, the corresponding q-values, and the ranks for the top gene sets.

Note

See the help page for calculate.NTk or calculate.NEk for example code that uses getPathwayStatistics

Author(s)

Lu Tian and Peter Park, with contributions from 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 1.1-0 Index]