Propagate a backward table

Propagates a kalisBackwardTable to an upstream variant. The table is updated in-place.

Usage

Backward(
  bck,
  pars,
  t = bck$l - 1,
  nthreads = min(parallel::detectCores(logical = FALSE), bck$to_recipient -
    bck$from_recipient + 1),
  beta.theta = FALSE
)

Arguments

bck

a kalisBackwardTable object, as returned by MakeBackwardTable().

pars

a kalisParameters object, as returned by Parameters().

t

a variant to move the backward table to. Must be less than or equal to current variant of bck. By default, it advances to the next variant upstream (or if an uninitialised table, to the last variant).

nthreads

if a scalar, the number of CPU cores to use. If a vector, launch as many threads as the length of the vector and attempt to pin the threads to those CPU cores (requires system to support thread affinity). By default uses the parallel package to detect the number of physical cores.

beta.theta

logical indicating whether the table should be returned in beta-theta space or in the standard space upon reaching the target variant t. See the Details section.

Value

There is nothing returned.

NOTE: for performance reasons, bck is updated in-place.

Details

Backward implements the backward algorithm to propagate the Li and Stephens rescaled hidden Markov model backward probabilities to a new target variant. Naturally, this can only propagate a table to variants upstream of its current position.

For mathematical details please see Section 2 of the kalis paper (Aslett and Christ, 2024). Note that the precise formulation of the backward equation is determined by whether the flag use.spiedel is set in the parameters provided in pars.

Beta-theta space

The rescaled HMM backward probabilities incorporate all of the haplotype relatedness information downstream from but NOT including the target variant, as is standard in the definition of HMM backward probabilities – we refer to this as "beta space", or "rescaled probability space." In contrast, the rescaled forward probabilities, naturally incorporate all of the haplotype relatedness information upstream from AND including the target variant. Setting beta.theta = TRUE incorporates the target variant (analogous to the rescaled forward probabilities) – we refer to this as "beta-theta space."

A backward table in beta-theta space (with beta.theta = TRUE) can be propagated to an upstream variant without incorporating that variant, thereby moving to beta space (beta.theta = FALSE), and vice versa. However, while a backward table in beta space (beta.theta = FALSE) can be updated to incorporate the current variant, a backward table that is already in beta-theta space can not move to beta space without changing variants – that would involve "forgetting" the current variant (see Examples).

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

MakeBackwardTable() to generate a backward table; Forward() for the analogous forward propagation function; CopyTable() to create a copy of table.

Examples

# Load the toy haplotype example and set toy parameters
data("SmallHaps")
data("SmallMap")

CacheHaplotypes(SmallHaps)

rho <- CalcRho(diff(SmallMap))
pars <- Parameters(rho)

# Create the backward table we want to propagate
bck <- MakeBackwardTable(pars)

# Calling Backward on this uninitialised table moves it to the last variant
Backward(bck, pars)
bck
#> Full Backward Table object for 300 haplotypes, in rescaled probability space. 
#>   Current variant = 400 
#>   Memory consumed: 724.13 kB 

# And again moves it to the next variant (etcetera)
Backward(bck, pars)
bck
#> Full Backward Table object for 300 haplotypes, in rescaled probability space. 
#>   Current variant = 399 
#>   Memory consumed: 724.13 kB 

# Or zoom to a particular variant
Backward(bck, pars, 150)
bck
#> Full Backward Table object for 300 haplotypes, in rescaled probability space. 
#>   Current variant = 150 
#>   Memory consumed: 724.13 kB 

# Now moving to variant 125 AND specifying "beta space" (though this is the
# default, just being very clear)
Backward(bck, pars, 125, beta.theta = FALSE)
bck
#> Full Backward Table object for 300 haplotypes, in rescaled probability space. 
#>   Current variant = 125 
#>   Memory consumed: 724.13 kB 

# Now just moving to "beta-theta space" (can be done with or without
# propagating to a new variant)
Backward(bck, pars, 125, beta.theta = TRUE)
bck
#> Full Backward Table object for 300 haplotypes, in beta-theta space. 
#>   Current variant = 125 
#>   Memory consumed: 724.13 kB 

# However, attempting to move from "beta-theta space" back to "beta space"
# without propagating is not possible (see Details).
# The following will give an error (hence wrapped in try())
try(Backward(bck, pars, 125, beta.theta = FALSE))
#> Error in Backward(bck, pars, 125, beta.theta = FALSE) : 
#>   Cannot move from beta-theta space to beta space without moving at least one variant.
bck
#> Full Backward Table object for 300 haplotypes, in beta-theta space. 
#>   Current variant = 125 
#>   Memory consumed: 724.13 kB