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
.