defaultGenerator {ChIPsim} | R Documentation |
Functions to generate defaults for makeFeatures
.
defaultGenerator() defaultTransition() defaultInit(prob=c(0.2, 0.05, 0, 0.25, 0.5), states=c("ReversePhasedFeature", "StableFeature", "PhasedFeature", "NFRFeature", "FuzzyFeature")) defaultLastFeat(isEnd = c(FALSE, rep(TRUE, 4)), states = c("ReversePhasedFeature", "StableFeature", "PhasedFeature", "NFRFeature", "FuzzyFeature"))
prob |
Numeric vector giving the initial state distribution. This will be normalised if the probabilities do not add up to 1. |
isEnd |
Logical vector indicating which states, i.e. features, are allowed to be last in the sequence. |
states |
Character vector of state names. |
These functions generate data structures that can be passed as arguments to makeFeatures
.
Using this set of functions will create a nucleosome positioning simulation. Some of the defaults
can be modified by passing different values to defaultInit
and defaultLastFeat
.
Return values are suitable as arguments generator
, transition
, init
and lastFeat
of
makeFeatures
. See the documentation of makeFeatures
for more detail.
Peter Humburg
set.seed(1) ## generate defaults generator <- defaultGenerator() transition <- defaultTransition() lastFeat <- defaultLastFeat() ## change the initial state distribution such that it ## always starts with a fuzzy feature init <- defaultInit(c(0, 0, 0, 0, 1)) ## now generate some features for a stretch of 1 million base pairs features <- makeFeatures(generator=generator, transition=transition, lastFeat=lastFeat, init=init, length=1e6)