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