rankPathways {sigPathway} | R Documentation |
Summarizes top pathways from pathway analyses.
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 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 and Peter Park, with contributions from 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