transforms {Umpire}

Transform functions

Description

normalOffset is a function that can be used as the TRANSFORM argument in an alterMean operation, which adds an offset to each value in the mean where the offset is chosen from a normal distribution.

invGammaMultiple is a function that can be used as the TRANSFORM argument in an alterSD operation, which multiplies each standard deviation by a positive value chosen from an inverse gamma distribution with parameters shape and scale.

Usage

normalOffset(x, delta, sigma)
invGammaMultiple(x, shape, rate)

Arguments

x

numeric vector of mean expression or standard deviation defined in the object

delta, sigma

numeric vector used as mean and/or sd parameters specifying the normal distribution

shape, rate

numeric vector used as shape and/or rate parameters specifying the gamma distribution. Must be positive.

Value

normalOffset returns a new vector, TO each element of which is added aN offset chosen from a normal distribution with parameters mean and sd.

invGammaMultiple returns a new vector, each element of which is multiplied by a positive value chosen from an inverse gamma distribution with parameters shape and scale.

Author(s)

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

See Also

alterMean, alterSD, RNGkind

Examples

nComp <- 10
nGenes <- 100
comp <- list()
for (i in 1:nComp) {
  comp[[i]] <- IndependentNormal(rnorm(nGenes/nComp, 6, 1.5),
                                 1/rgamma(nGenes/nComp, 44, 28))
}
myEngine <- Engine(comp)
nrow(myEngine)
nComponents(myEngine)
summary(myEngine)
myData <- rand(myEngine, 5)
dim(myData)
summary(myData)
MEAN <- 2
SD <- 2
myEngine.alterMean <- alterMean(myEngine,
                                function(x) normalOffset(x, MEAN, SD))
myData.alterMean <- rand(myEngine.alterMean, 5)
summary(myData.alterMean)
RATE <- 1
SHAPE <- 2
myEngine.alterSD <- alterSD(myEngine,
                            function(x) invGammaMultiple(x, SHAPE, RATE))
myData.alterSD <- rand(myEngine.alterSD, 5)
summary(myData.alterSD)