hyperGtable {GOstats} | R Documentation |
Use the summary
method on a GOHyperGResult
object.
Output a table from a call to GOHyperG
.
hyperGtable(probids, lib, type = "MF", pvalue = 0.05, min.count = 10, save = FALSE, output = TRUE, filename = NULL, universe = NULL)
probids |
A vector of Affymetrix probe IDs |
lib |
An annotation package (e.g., hgu95av2 ) |
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. |
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. |
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). |
This function will take a vector of Affymetrix IDs and output a
data.frame
containing information on all GO terms that are found
significant in a call to GOHyperG
.
A data.frame
containing the following columns:
GO Term - The GOID associated with a given GO term
Description - The description for that GO term
p-values - The p-value associated with that GO term
Number significant - The number of genes in the vector of Affymetrix IDs
with that particular GO term
Number on chip - The number of genes on the Affymetrix chip with that
particular GO term.
James W. MacDonald <jmacdon@med.umich.edu>
## Not run: library("hgu95av2") probids <- ls(hgu95av2GENENAME)[1:10] hyperGtable(probids, "hgu95av2", save = TRUE, output = FALSE) ## End(Not run)