rPairedNegBin.Rd
A gene expression matrix of counts with N
features and
length(n)
pairs of samples.
The first pair corresponds to the two first column and so on.
The total number of samples is 2*n
The distribution of the first component is negative binomial
with mean mu1
and dispersion parameter 1/size1
(the variance
is equal to mu1 + (mu1^2)/size1
.
For the genes (rows) in gs
the distribution is the sum of the
first generated value plus a random count with negative binomial distribution
with mean mu2
and dispersion 1/size2.
For the genes (rows) not in gs
the distribution of the second component
is the sum of the first generated value
plus a random count with negative binomial distribution with mean
mu3
and dispersion 1/size3.
The matrix outlier
contains in the first column the indices of rows and in
the second column the indices of pairs. For the pairs of counts in outlier
the first component follows a negative binomial distribution with mean
mu1
and dispersion 1/size1 and the second component is equal to the
first one plus a random count with negative binomial distribution with mean
mu4
and dispersion 1/size4.
rPairedNegBin(n, N, mu1, size1, mu2, size2, mu3, size3, mu4, size4, gs = NULL, outlier = NULL)
n | Number of pairs |
---|---|
N | Number of genes |
mu1 | Mean of the first component |
size1 | 1/size1 is the dispersion of the first component |
mu2 | Mean of the random count added to the first generated value on the significant genes |
size2 | 1/size2 is the dispersion of the random count added to the first generated value on the significant genes |
mu3 | Mean of the random count added to the first generated value on the non significant genes |
size3 | 1/size3 is the dispersion of the random count added to the first generated value on the non significant genes |
mu4 | Mean of the random count added to the first generated value
on the outlier genes given in |
size4 | 1/size4 is the dispersion of the random count added to the first generated value on the outlier genes |
gs | Significant gene set (a subset of rows in 1:N) |
outlier | Matrix (rows as genes and pairs as samples) where the corresponding pair of counts are an outlier gs == NULL correspond with no differential expression |