rPairedNB.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 (control) 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 of the second
component of the pair (case) is a negative binomial distribution
with mean mu2
and dispersion 1/size2.
For the genes (rows) not in gs
(significant genes) the
distribution of the second component is negative binomial 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
follows a negative binomial distribution with mean
mu4
and dispersion 1/size4.
rPairedNB(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 |