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Read genomic data

Source: R/read_genome.R
read_genome.Rd

Detect a supported genomic format and route it to the appropriate format-specific reader. The generic interface uses the defaults of each read_*() function; call that reader directly when additional control is required. Package-native tabular inputs are normalized with the internal as_tidy_genome() helper. The function uses read_parquet or CoreArray Genomic Data Structure (GDS) file system.

Usage

read_genome(
  data,
  strata = NULL,
  columns = NULL,
  allow.dup = FALSE,
  check = TRUE,
  import.metadata = TRUE,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE
)

Arguments

data

A file in the working directory ending with .arrow.parquet or .gds, a TSV or legacy RAD/FST file, or an existing wide/tidy genomic table.

strata

Optional strata data or filename passed to readers that support it. Default: strata = NULL.

columns

(optional) For arrow.parquet file. Column names to read. The default is to read all all columns. Default: columns = NULL.

allow.dup

(optional, logical) To allow the opening of a GDS file with read-only mode when it has been opened in the same R session. Default: allow.dup = FALSE.

check

(optional, logical) Verify that GDS number of samples and markers match. Default: check = TRUE.

import.metadata

Logical. Retain columns in addition to the standard genomic columns when normalizing tabular input. Default: import.metadata = TRUE.

parallel.core

Number of processor cores passed to readers that support parallel processing. Default: parallel.core = parallel::detectCores() - 1.

verbose

Logical. Display progress messages. For GDS input, the current number of samples and markers and a summary of active filters are displayed. Default: verbose = TRUE.

Value

A tidy genomic data frame or GDS object (with read/write permissions) in the global environment.

Details

For GDS file system, read_genome will open the GDS connection file set the filters (variants and samples) based on the info found in the file.

Dependencies

Required package dependencies are declared in DESCRIPTION and installed with genometranslator. Run genometranslator_dependencies() to inspect core packages, optional packages, and external executables.

This dispatcher uses the dependencies documented by the selected format-specific read_*() function. Legacy FST/RAD files additionally require the optional CRAN package fst; VCF preparation may require the optional bcftools executable.

See also

arrow GDS read_genome

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
shark <- genometranslator::read_genome(data = "data.shark.gds")
turtle <- genometranslator::read_genome(data = "data.turtle.arrow.parquet")
} # }