Chromosome painting using genealogies.

This function outputs the first coalescence with an individual from a pre-specified group identity along the genome. If the first such coalescnece involves several copying candidates, a random haplotype is chosen. Output is in GLOBEtrotter format.

Painting(
  file_anc,
  file_mut,
  file_map,
  file_out,
  poplabels,
  blgsize = NULL,
  pops = NULL,
  chrs = NULL
)

Arguments

file_anc: Filename of anc file. If chrs is specified, this should only be the prefix, resulting in filenames of ${file_anc}_chr${chr}.anc(.gz).
file_mut: Filename of mut file. If chrs is specified, this should only be the prefix, resulting in filenames of ${file_anc}_chr${chr}.anc(.gz).
file_map: File prefix of recombination map.
file_out: File prefix of output files
poplabels: Filename of poplabels file
blgsize: (Optional) SNP block size in Morgan. Default is 0.05 (5 cM). If blgsize is 1 or greater, if will be interpreted as base pair distance rather than centimorgan distance.
pops: (Optional) Populations for which data should be extracted. Names need to match the second column of the poplabels file
chrs: (Optional) Vector of chromosome IDs

Value

void. Write three files idfile, paint, rec to disc.

Examples

file_anc  <- system.file("sim/msprime_ad0.8_split250_1_chr1.anc.gz", package = "twigstats")
file_mut  <- system.file("sim/msprime_ad0.8_split250_1_chr1.mut.gz", package = "twigstats")
poplabels <- system.file("sim/msprime_ad0.8_split250_1.poplabels", package = "twigstats")
file_map  <- system.file("sim/genetic_map_combined_b37_chr1.txt.gz", package = "twigstats")

#define populations to paint against:
pops <- c("P1","P2","P3","P4")

Painting(file_anc, file_mut, file_map, file_out = "test", poplabels, blgsize = 1e-5)