testGeneFamilies.hypergeometric {ShotgunFunctionalizeR} | R Documentation |
Test for significant gene families using the hypergeometric model.
testGeneFamilies.hypergeometric(data)
data |
$2times n$ matrix containing counts |
testGeneFamilies.binomial
performs an exact hypergeometric test for each row of
in the data matrix. Under the assumption that the counts from both
metagenomes follows a multinomial distribution, the procedure test whether
$p_{i1}=p_{i2}$ for each row $i=1, ..., n$. If $X_{i1}$ and $X_{i2}$ are
the counts for row $i$ and metagenome 1 and 2 respectively, it follows that
[
X_{i1}|X_{i1}+X_{i2}=n sim Hyper(M_1+M_2, M_1, n)
]
where $M_1$ and $M_2$ are the total number of counts in metagenome 1 and 2
respectively. The function testGeneFamilies.binomial
provides a faster binomial approximation.
testGeneFamilies.hypergeometic
is usually called
implicitly by using the 'binomial' method in testGeneFamilies
.
testGeneFamilies.binomial
returns a list with the following
elements
PValues |
A list of p-values |
Rankings.detail |
A list additional elements containing details about the ranking |
testGeneFamilies
,
testGeneFamilies.binomial
,
testGeneFamilies.gaussian
,
testGeneFamilies.poisson