Create deterministic GLIMPSE2 imputation chunks — rglimpse2

Invokes GLIMPSE2_chunk once. All paths are explicit and the output file must not already exist.

Usage

rglimpse2_chunk(
  input_sites,
  region,
  output_chunks,
  executable,
  genetic_map,
  seed,
  threads = 1L,
  algorithm = c("sequential", "recursive"),
  window_cm = 2.5,
  window_mb = 2,
  window_count = 20000L,
  buffer_cm = 0.5,
  buffer_mb = 0.4,
  buffer_count = 2000L,
  sparse_maf = 0.001,
  log = character()
)

Arguments

input_sites: Absolute VCF/BCF sites path.
region: Contig or genomic interval to split.
output_chunks: Absolute output chunk-table path.
executable: Absolute GLIMPSE2_chunk path.
genetic_map: Absolute genetic-map path, such as one returned by rglimpse2_genetic_map().
seed: Non-negative random seed.
threads: Positive worker count.
algorithm: Chunking algorithm.
window_cm, window_mb: Positive minimum window sizes.
window_count: Positive minimum window variant count.
buffer_cm, buffer_mb: Positive minimum buffer sizes.
buffer_count: Positive minimum buffer variant count.
sparse_maf: Rare-variant threshold in [0, 0.5).
log: Empty or one absolute log output path.

Value

RGlimpse2RunResult or an RGlimpse2ErrorValue.