Given a ptw object, predict either the signal at a certain
warped time, or the warped time itself.
Usage
## S3 method for class 'ptw'
predict(object, newdata, what = c("response", "time"),
RTref = NULL, ...)
Arguments
object
An object of class "ptw"
newdata
Optional vector or matrix of new data points. If
what equals "response", the new data should be a vector or
matrix of intensities. If what equals "time", the new data is
a vector of time points (a matrix of time points makes no sense...).
what
Either "response", in which case the function returns the
warped signal, or "time", and then the function returns the warped
time axis. That is, the time point in the warped sample
corresponding to the given time point in the original sample.
RTref
Optional vector of retention times in the reference.
...
Further arguments, at the moment not used.
Value
The function returns a matrix (possibly containing only one
row) of either warped time points or signals, warped according to the
warping function defined in object. When warping signals
individually, predict.ptw will check the dimension of
newdata: if this is a vector or a matrix of one row, every
single warping function will be applied to the one row. If the
number of rows equals the number of warping functions, each row will
be warped with its corresponding function. If the number of rows does
not match the number of warping functions and is not equal to one, an
error is given.
Author(s)
Ron Wehrens
References
Eilers, P.H.C. "Parametric Time Warping." Anal. Chem., 2004, 76, 404-411
Bloemberg, T.G. et al. "Improved parametric time warping for
proteomics." Chemom. Intell. Lab. Syst., 2010, 104, pp. 65-74
See Also
ptw
Examples
data(gaschrom)
## Global warping: all samples warped with the same function
ref <- gaschrom[1,]
samp <- gaschrom[14:16,]
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "global")
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
## plot predicted warped signal directly
matlines(t(predict(gp)), lty = 2, col = 1:3)
## plot original signal at warped time axis
matlines(t(predict(gp, newdata = 2001:2600, what = "time")),
t(samp[,2001:2600]), col = 1:3, lwd = 3, lty = 2) ## OK
## Individual warping: all samples warped individually
gp <- ptw(ref, samp, init.coef = c(0, 1), warp.type = "indiv")
predict(gp, what = "time", newdata = 2001:2600)
matplot(t(samp), type = "l", xlim = c(2200, 2400), lty = 1, col = 1:3)
lines(ref, type = "l", col = "gray", lwd = 2)
matlines(t(predict(gp, what = "time")),
t(samp), col = 1:3, lty = 2)
## How would samples 11:13 be warped using the coefficients from samples
## 14:16 (silly but just to make the point)?
samp.pred <- predict(gp, what = "response", newdata = gaschrom[11:13,])
matplot(t(samp), type = "l", lty = 1, col = 1:3, xlim = c(2200, 2400))
lines(ref, type = "l", col = "gray")
matlines(t(samp.pred), type = "l", lty = 2)