Retrieve haplotypes from the memory cache, converting the raw binary into an integer 0/1 matrix for inspection and use in R.
Arguments
- loci.idx
which variants to retrieve from the cache, specified as a (vector) index. This enables specifying variants by offset in the order they were loaded into the cache (from 1 to the number of variants).
- hap.idx
which haplotypes to retrieve from the cache, specified as a (vector) index. This enables specifying haplotypes by offset in the order they were loaded into the cache (from 1 to the number of haplotypes).
Value
A matrix of 0/1 integers with length(loci.idx) rows and length(hap.idx) columns, such that haplotypes appear in columns.
Details
To achieve higher performance, kalis internally represents haplotypes in an efficient raw binary format in memory which cannot be directly viewed or manipulated in R. This function enables you to copy whole or partial views of haplotypes/variants out of this low-level format and into a standard R matrix of 0's and 1's.
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
CacheHaplotypes() to fill the memory cache with haplotype data.
Examples
# For the purposes of an example, fill the cache with random haplotypes ...
n.haps <- 100
n.vars <- 200
haps <- matrix(sample(0:1, n.haps*n.vars, replace = TRUE),
nrow = n.vars, ncol = n.haps)
CacheHaplotypes(haps)
#> Warning: haplotypes already cached ... overwriting existing cache.
# ... and confirm we can read a chosen portion back. Try to read back the
# 10th and 11th haplotypes from variants 50 to 150 inclusive
res <- QueryCache(50:150, 10:11)
all(res == haps[50:150, 10:11])
#> [1] TRUE