Summarizes top pathways from one of the pathway analyses (i.e.,
a list from the output of
a list containing the source, title, and probe sets associated with each curated pathway
a list containing three vectors from the output of
a character vector of length 1 giving the name of
the pathway analysis used in making
an integer indicating the number of top gene sets to consider when ranking the top pathways
This function ranks the statistics given in
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,
the corresponding q-values, and the numerical ranks for the top gene sets.
See the help page for
calculate.NGSk for example code that
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.
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