e03-IndependentNormal-class: The "IndependentNormal" Class

In Umpire: Simulating Realistic Gene Expression and Clinical Data

Description

The IndependentNormal class is a tool used to generate gene expressions that follow independent normal distribution.

Usage

IndependentNormal(mu,sigma)
## S4 method for signature 'IndependentNormal'
alterMean(object, TRANSFORM, ...)
## S4 method for signature 'IndependentNormal'
alterSD(object, TRANSFORM, ...)
## S4 method for signature 'IndependentNormal'
nrow(x)
## S4 method for signature 'IndependentNormal'
rand(object, n, ...)
## S4 method for signature 'IndependentNormal'
summary(object, ...)

Arguments

mu	numeric vector specifying the mean expression values
sigma	numeric vector specifying the standard deviation of the gene expression values
object, x	object of class IndependentNormal
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 specifying number of samples to be simulated
...	extra arguments for generic or plotting routines

Details

Note that we typically work on expression value with its logarithm to some appropriate base. That is, the independent normal should be used on the logarithmic scale in order to construct the engine.

Objects from the Class

Objects can be created by using the IndependentNormal generator function. The object of class IndependentNormal contains the mean and standard deviation for the normal distribution

Slots

mu:

see corresponding argument above

sigma:

see corresponding argument above

Methods

alterMean(object, TRANSFORM, ...)

Takes an object of class IndependentNormal, loops over the mu slot, alters the mean as defined by TRANSFORM function, and returns an object of class IndependentNormal with altered mu.

alterSD(object, TRANSFORM, ...)

Takes an object of class IndependentNormal, loops over the sigma slot, alters the standard deviation as defined by TRANSFORM function, and returns an object of class IndependentNormal with altered sigma.

nrow(x)

Returns the number of genes (i.e, the length of the mu vector).

rand(object, n, ...)

Generates nrow(IndependentNormal)*n matrix representing gene expressions of n samples following the normal distribution captured in the object of IndependentNormal.

summary(object, ...)

Prints out the number of independent normal random variables in the object of IndependentNormal.

Author(s)

Kevin R. Coombes [e-mail], Jiexin Zhang [e-mail],

See Also

Engine, IndependentLogNormal, MVN

Examples

showClass("IndependentNormal")
nGenes <- 20
mu <- rnorm(nGenes, 6, 1)
sigma <- 1/rgamma(nGenes, rate=14, shape=6)
ind <- IndependentNormal(mu, sigma)
nrow(ind)
summary(ind)
if (any(mu - ind@mu)) {
  print('means do not match')
} else {
  print('means verified')
}
if (any(sigma - ind@sigma)) {
  print('standard deviations do not match')
} else {
  print('sd verified')
}
x <- rand(ind, 3)
print(dim(x))
print(summary(x))
print(paste("'ind' should be valid:", validObject(ind)))
ind@sigma <- 1:3 # now we break it
print(paste("'ind' should not be valid:", validObject(ind, test=TRUE)))
rm(nGenes, mu, sigma, ind, x)

Umpire documentation built on Oct. 20, 2020, 3:01 a.m.