extract_coverage: check_coverage

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

check_coverage

Description

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

Usage

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.

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.