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

Description Usage Arguments Details Value Note Author(s) References

View source: R/rankPathways.R

Description

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

Usage

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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


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