| GOstats-defunct {GOstats} | R Documentation |
The functions or variables listed here are no longer part of GOstats as they are not needed (any more).
combGOGraph(g1, g2)
hyperGtable(probids, lib, type="MF", pvalue=0.05,
min.count=10, save = FALSE, output = TRUE,
filename = NULL, universe = NULL)
hyperG2Affy(probids, lib, type="MF", pvalue=0.05,
min.count=10, universe = NULL)
g1 |
A graph |
g2 |
A graph |
probids |
A vector of Affymetrix probe IDs |
lib |
An annotation package (e.g., hgu95av2.db) |
type |
One of "MF", "CC", "BP", indicating molecular function, cellular component, or biological process, respectively. |
pvalue |
The significance level used to choose GO terms |
min.count |
The minimum number of a given GO term that must be on the chip in order to choose that GO term. This protects against very low p-values that result from the situation where there are very few genes with a given GO term on the chip, but one or two are found in the set of significant genes. |
universe |
A character vector of unique Entrez Gene identifiers
or NULL. This is the population (the urn) of the
Hypergeometric test. When NULL (default), the population is
all Entrez Gene ids in the annotation package that have a GO term
annotation in the specified GO category (see GOHyperG for
more details). |
save |
Boolean - Set to TRUE to save the resulting data.frame. |
output |
Boolean - Set to TRUE to output the resulting
data.frame as a text file. |
filename |
If output is set to TRUE, give the file name
for the output file. |
combGOGraph was replaced by join.
hyperGtable was replaced by summary.
hyperG2Affy was replaced by probeSetSummary.