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Copy Forward/Backward tables

Source: R/TableMaker.R
CopyTable.Rd

Copies the contents of one forward/backward table into another.

Usage

CopyTable(to, from)

Arguments

to

a kalisForwardTable or kalisBackwardTable object which is to be copied into.

from

a kalisForwardTable or kalisBackwardTable object which is to be copied from.

Details

The core code in kalis operates on forward and backward tables at a very low level, both for speed (using low level CPU vector instructions) but also to avoid unnecessary memory copies since these tables will tend to be very large in serious genetics applications. As a result, if you attempt to copy a table in the standard idomatic way in R:

fwd2 <- fwd

then these two variables merely point to the same table: running the forward algorithm on fwd would result in fwd2 also changing.

This function is therefore designed to enable explicit copying of tables.

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 tables which can be copied into.

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 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:
fwd2 <- fwd
Forward(fwd, pars, 20)

# Both tables are now at variant 20
fwd
#> Full Forward Table object for 300 haplotypes. 
#>   Current variant = 20 
#>   Memory consumed: 723.98 kB 
fwd2
#> Full Forward Table object for 300 haplotypes. 
#>   Current variant = 20 
#>   Memory consumed: 723.98 kB 

# Instead, to copy we create another table and use this function
fwd2 <- MakeForwardTable(pars)
CopyTable(fwd2, fwd)

# Now propagate fwd again
Forward(fwd, pars, 30)

# But notice this fwd2 wasn't affected
fwd
#> Full Forward Table object for 300 haplotypes. 
#>   Current variant = 30 
#>   Memory consumed: 723.98 kB 
fwd2
#> Full Forward Table object for 300 haplotypes. 
#>   Current variant = 20 
#>   Memory consumed: 723.98 kB