check_coverage

Check that the coverage info is in the GDS. By default, it will look for the DP and AD info in the FORMAT field.

Extract coverage information from a GDS file

check_coverage(
  gds,
  genotypes.metadata.check = FALSE,
  stacks.haplo.check = FALSE,
  dart.check = FALSE
)

extract_coverage(
  gds,
  individuals = TRUE,
  markers = TRUE,
  dp = TRUE,
  ad = TRUE,
  coverage.stats = c("sum", "mean", "median", "iqr"),
  subsample.info = 1,
  verbose = TRUE,
  parallel.core = TRUE
)

Arguments

gds

The gds object.

genotypes.metadata.check

(optional, logical) Look for already extracted coverage information in the radiator genotypes_metadata field of the GDS. Default: genotypes.metadata.check = FALSE.

stacks.haplo.check

(optional, logical) stacks haplotypes VCF header is baddly generated. It will say you have Read and allele Depth info, but you don't. Default: stacks.haplo.check = FALSE.

dart.check

(optional, logical) DArT have different reporting for coverage information. Will no longer report the average coverage stats from 1 and 2-rows DArT format. Default: dart.check = FALSE.

individuals

(optional, logical) Default: individuals = TRUE.

markers

(optional, logical) Default: markers = TRUE.

dp

(optional, logical) Default: dp = TRUE.

ad

(optional, logical) Default: ad = TRUE.

coverage.stats

(optional, character string). Choice of stats to use with coverage. Default: coverage.stats = c("sum", "mean", "median", "iqr").

subsample.info

(optional, double) Default: subsample.info = 1. The subsample proportion used (e.g. 0.3 or none the default).

verbose

(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.

parallel.core

(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.