discont_basis: Provides set of basis functions on either side of a time...

In NelleV/moanin: An R Package for Time Course RNASeq Data Analysis

Description

Provides set of basis functions on either side of a time point, allowing for a discontinuity in the fitted functions

Usage

discont_basis(
  timepoints,
  discont_point,
  knots = NULL,
  dfPre = NULL,
  dfPost = dfPre,
  degree = 3,
  intercept = TRUE,
  type = c("ns", "bs")
)

Arguments

timepoints	vector of numeric timepoints for which the splines basis will be evaluated
discont_point	a single numeric value that represents where the discontinuity should be
knots	passed to ns or bs. If not NULL, should give knots on either side of discon_point as single vector – they will be separated in the call to discon_point
dfPre	the df for the basis functions defined before the discontinuity point
dfPost	the df for the basis functions defined after the discontinuity point
degree	passed to bs (if applicable)
intercept	Whether to include an intercept (vector of all 1s) for each side of the discontinuity. Note this is different than the argument intercept of either bs or ns, which is set to FALSE.
type	either "ns" or "bs" indicating which splines basis function should be used.

Examples

x<-seq(0,10,length=100)
basis<-discont_basis(x,discont_point=3, dfPre=3, dfPost=4, intercept=TRUE)
# Plot of the basis functions
par(mfrow=c(3,3))
for(i in 1:ncol(basis)){
   plot(x,basis[,i],type="l")
   abline(v=3,lty=2)
}
# Use it in a moanin_model object instead of ns/bs:
data(exampleData)
moanin <- create_moanin_model(data=testData, meta=testMeta,
    spline_formula=~Group:discont_basis(Timepoint,dfPre=3,
        dfPost=3,discont=20,intercept=TRUE)+0,
    degrees_of_freedom=6)

NelleV/moanin documentation built on July 28, 2021, 7:34 p.m.