Resets the provided forward/backward table so it can propagate from the start/end of the Li and Stephens hidden Markov model.
Details
It is much faster to reset a forward/backward table rather than remove and make a new one. This function marks a table as reset so that it will be propagated as if freshly allocated.
References
Aslett, L.J.M. and Christ, R.R. (2024) "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R", BMC Bioinformatics, 25(1). Available at: doi:10.1186/s12859-024-05688-8 .
See also
MakeForwardTable(), MakeBackwardTable() to create fresh tables.
Examples
# Load the toy haplotype example and set toy parameters
data("SmallHaps")
data("SmallMap")
CacheHaplotypes(SmallHaps)
#> Warning: haplotypes already cached ... overwriting existing cache.
rho <- CalcRho(diff(SmallMap))
pars <- Parameters(rho)
# Create the forward table we want to propagate
fwd <- MakeForwardTable(pars)
# Move to variant 10
Forward(fwd, pars, 10)
fwd
#> Full Forward Table object for 300 haplotypes.
#> Current variant = 10
#> Memory consumed: 723.98 kB
# This does **NOT** work as intended, cannot reverse from variant 10:
try(Forward(fwd, pars, 5))
#> Error in Forward(fwd, pars, 5) :
#> The forward table provided is for variant position 10 which is already past requested variant 5
# Could reset the table though:
ResetTable(fwd)
Forward(fwd, pars, 5)
fwd
#> Full Forward Table object for 300 haplotypes.
#> Current variant = 5
#> Memory consumed: 723.98 kB