Description Usage Arguments Details Objects from the Class Slots Methods Author(s) See Also Examples
The MVN
class is a tool used to generate gene expressions that
follow multivariate normal distribution.
1 2 3 4 5 6 7 8 9 10 11 12 13  MVN(mu, Sigma, tol = 1e06)
covar(object)
correl(object)
## S4 method for signature 'MVN'
alterMean(object, TRANSFORM, ...)
## S4 method for signature 'MVN'
alterSD(object, TRANSFORM, ...)
## S4 method for signature 'MVN'
nrow(x)
## S4 method for signature 'MVN'
rand(object, n, ...)
## S4 method for signature 'MVN'
summary(object, ...)

mu 
numeric vector representing kdimensional means 
Sigma 
numeric kbyk covariance matrix containing the measurement of the linear coupling between every pair of random vectors 
tol 
numeric scalar roundoff error that will be tolerated when assessing the singularity of the covariance matrix 
object, x 
object of class 
TRANSFORM 
function that takes a vector of mean expression or standard deviation and returns a transformed vector that can be used to alter the appropriate slot of the object. 
n 
numeric scalar representing number of samples to be simulated 
... 
extra arguments for generic or plotting routines 
The implementation of MVN
class is designed for efficiency when
generating new samples, since we expect to do this several times.
Basically, this class separates the mvrnorm
function from the
MASS package into several steps. The computationally expensive step
(when the dimension is large) is the eigenvector decomposition of the
covariance matrix. This step is performed at construction and the
pieces are stored in the object. The rand
method for MVN
objects contains the second half of the mvrnorm
function.
Note that we typically work on expression value with its logarithm to some appropriate base. That is, the multivariate normal should be used on the logarithmic scale in order to contruct engine.
alterMean
for an MVN
simply replaces the appropriate slot by
the transformed vector. alterSD
for an MVN
is trickier,
because of the way the data is stored. In order to have some hope of getting
this correct, we work in the space of the covariance matrix, Sigma.
If we let R denote the correlation matrix and let Delta be the
diagonal matrix whose entries are the individual standard deviations, then
Sigma = Delta \%*\% R \%*\% Delta.
So, we can change the standard deviations by replacing Delta in this
product. We then construct a new MVN
object with the old mean vector
and the new covariance matrix.
covar
and correl
functions calculate the covariance matrix
and correlation matrix underlies the covariance matrix for the objects of
class MVN
, respectively. We have four assertions as shown below,
and will be tested in the examples section:
covar
should return the same matrix that was used
in the function call to construct the MVN
object.
After applying an alterMean
method, the
covariance matrix is unchanged.
The diagonal of correlation matrix consists of all ones.
After applying an alterMean
or an alterSD
method, the
correlation matrix is unchanged.
Although objects of the class can be created by a direct call to
new, the preferred method is to use the
MVN
generator function.
mu
:numeric vector containing the kdimentional means
lambda
:numeric vector containing the square roots of eigenvalues of the covariance matrix
half
:numeric matrix with k*k dimensions whose columns contain the eigenvectors of the covariance matrix
Takes an object of class
MVN
, loops over the mu
slot, alters the mean as defined
by TRANSFORM function, and returns an object of class MVN
with
altered mu
.
Takes an object of class
MVN
, works on the diagonal matrix of the covariance matrix, alters
the standard deviation as defined by TRANSFORM function, and reconstructs
an object of class MVN
with the old mu
and
reconstructed covariance matrix.
Returns the number of genes (i.e, the length of the
mu
vector).
Generates nrow(MVN)*n matrix
representing gene expressions of n
samples following the
multivariate normal distribution captured in the object of MVN
.
Prints out the number of
multivariate normal random variables in the object of MVN
.
Returns the covariance matrix of the object of
class MVN
.
Returns the correlation matrix of the object of
class MVN
.
Kevin R. Coombes krc@silicovore.com, Jiexin Zhang jiexinzhang@mdanderson.org,
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28  showClass("MVN")
## Not run:
tolerance < 1e10
## Create a random orthogonal 2x2 matrix
a < runif(1)
b < sqrt(1a^2)
X < matrix(c(a, b, b, a), 2, 2)
## Now choose random positive squaredeigenvalues
Lambda2 < diag(rev(sort(rexp(2))), 2)
## Construct a covariance matrix
Y < t(X)
## Use the MVN constructor
marvin < MVN(c(0,0), Y)
## Check the four assertions
print(paste('Tolerance for assertion checking:', tolerance))
print(paste('Covar assertion 1:',
all(abs(covar(marvin)  Y) < tolerance)))
mar2 < alterMean(marvin, normalOffset, delta=3)
print(paste('Covar assertion 2:',
all(abs(covar(marvin)  covar(mar2)) < tolerance)))
print(paste('Correl assertion 1:',
all(abs(diag(correl(marvin))  1) < tolerance)))
mar3 < alterSD(marvin, function(x) 2*x)
print(paste('Correl assertion 1:',
all(abs(correl(marvin)  correl(mar2)) < tolerance)))
rm(a, b, X, Lambda2, Y, marvin, mar2, mar3)
## End(Not run)

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.