HyperGParams, compute Hypergeomtric
p-values for over or under-representation of each term in the
specified category among the specified gene set.
hyperGTest(p)HyperGParams. This parameter object
determines the category of interest (e.g., GO or KEGG) as well as the
gene set.HyperGResult instance.
HyperGParams is all that will be needed. This
method follows a template pattern. To add support for a new FOO
category type, a developer would need to create a
FooHyperGParams subclass and then define two methods
specialized to the new subclass that get called from inside
hyperGTest: universeBuilder and
categoryToEntrezBuilder.geneIds slot of p define the
selected set of genes. The universe of gene ids is determined by the
chip annotation found in the annotation slot of p. Both
the selected genes and the universe are reduced by removing
identifiers that do not have any annotations in the specified
category.
For each term in the specified category that has at least one
annotation in the selected gene set, we determine how many of its
annotations are in the universe set and how many are in the selected
set. With these counts we perform a Hypergeometric test using
phyper. This is equivalent to using Fisher's exact test.
It is important that the correct chip annotation data package be
identified as it determines the universe of gene identifiers and is
often used to determine the mapping between the category term and the
gene identifiers.
For S. cerevisiae if the annotation slot of p is set to
'"org.Sc.sgd"' then comparisons and statistics are computed using common
names and are with respect to all genes annotated in the S. cerevisiae
genome not with respect to any microarray chip. This will *not* be
the right thing to do if you are working with a yeast microarray.
HyperGResult-class
HyperGParams-class
GOHyperGParams-class
KEGGHyperGParams-class