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Convert Local-Ancestry Tracts Format from GDS to Text

convert_gds_to_txt.Rd

Converts ancestry-specific dosage and hapcount matrices stored in a tracts GDS file into tab-delimited text files (plain or gzipped).

Usage

convert_gds_to_txt(
  gds_path,
  output_prefix = NULL,
  output_format = "txt.gz",
  chunk_size = 1024L
)

Arguments

gds_path

Character; input tracts GDS path.

output_prefix

Character or NULL; output file prefix. If NULL (default), uses the input filename prefix in the same directory as gds_path.

output_format

Character; output format, one of "txt" or "txt.gz" (default).

chunk_size

Integer; number of variants processed per chunk. Default is 1024; higher values can improve speed but increase memory usage.

Value

Invisibly returns NULL. For each ancestry k, writes two files: <output_prefix>.anc{k}.dosage.txt(.gz) and <output_prefix>.anc{k}.hapcount.txt(.gz).

Details

Output tables contain columns CHROM, POS, ID, REF, ALT, followed by one column per sample from sample.id in the input GDS.