selectGeneSets {sigPathway} | R Documentation |
Selects gene sets to be analyzed in pathway analysis based on minimum and maximum number of probe sets to consider per pathway.
selectGeneSets(G, probeID, minNPS = 20, maxNPS = 500)
G |
a list containing the source, title, and probe sets associated with each curated pathway |
probeID |
a character vector containing the names of probe sets associated with a matrix of expression values |
minNPS |
an integer specifying the minimum number of probe sets
in probeID that should be in a gene set |
maxNPS |
an integer specifying the maximum number of probe sets
in probeID that should be in a gene set |
This function selects the appropriate pathways from a large, curated
list based on the minimum and maximum number of probe sets that should
be considered in a gene set. It creates three vectors: nprobesV
and indexV
representing a sparse indicator matrix and
indGused
indicating which gene sets were selected from
G
.
A list containing
nprobesV |
an integer vector indicating the number of probe sets
in probeID that is in each selected gene set |
indexV |
an integer vector containing positions for each 1s in the sparse indicator matrix |
indGused |
an integer vector indicating which pathways in
G were chosen |
See the help page for calculate.NTk
or calculate.NEk
for example code that uses getPathwayStatistics
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