rankPathways: Summarizes Top Pathways from Pathway Analyses
In sigPathway: Pathway Analysis

Description Usage Arguments Details Value Note Author(s) References

Summarizes top pathways from pathway analyses.

1 2	rankPathways(res.A, res.B, G, tab, phenotype, gsList, ngroups, methodNames = NULL, npath = 25, allpathways = FALSE)

`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
`tab`	a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively
`phenotype`	a numeric (or character if `ngroups` >= 2) vector indicating the phenotype
`gsList`	a list containing three vectors from the output of the `selectGeneSets` function
`ngroups`	an integer indicating the number of groups in the matrix
`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
`allpathways`	a boolean to indicate whether to include the top `npath` pathways from each statistic or just consider the top `npath` pathways (sorted by the sum of ranks of both statistics) when generating the summary table

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)

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.

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

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.