import: Imports a htslib-compatible variant-call file into Tomahawk

In mklarqvist/rtomahawk: Tools for computing, querying and storing linkage-disequilibrium data

Description

Some additional details about this S4 generic and its methods. The extra blank line between this section and the title is critical for roxygen2 to differentiate the title from the description section.

Usage

import(input = "character", output = "character",
  missingness = "numeric", block_size = "integer",
  compression_level = "integer", filter_univariate = "logical", ...)

Arguments

input	Input string pointing to the htslib-compatible file.
output	Output string pointing to the Tomahawk file.
block_size	Advanced use: number of variants packed in each internal Tomahawk block. This could have potential impact on the parallel throughput capabilities of Tomahawk on large cohorts.
compression_level	Compressing level in the range [1, 22] for compressing the Tomahawk file. Larger numbers results in smaller resting file size at the expense of importing speeds. Decompressing speeds are largely unaffected by the compression level.
filter_univariate	Logical (boolean) flag set to TRUE if univariate (monomorphic) should be filtered out. If this flag is set to FALSE then monomorphic sites are left in the file. The recommendation is to remove these as they contribute no information.
missnigness	Numerical value in the range [0, 1] representing the largest fraction of missing values that are allowed. If the threshold is violated then the variant site is filtered out.

Value

Returns a twk class with the file handle pointing to the newly imported Tomahawk file.

Author(s)

Marcus D. R. Klarqvist <[e-mail]> | <https://mdrk.me>

See Also

twk_data, twk_header, twk_filter, and twk

Examples

# This example assumes you have a Tomahawk file called "1kgp3_chr20.bcf" in
# your current working directory.
twk <- import("1kgp3_chr20.bcf","~/Downloads/1kgp3_chr20")
twk

mklarqvist/rtomahawk documentation built on May 16, 2019, 5:01 a.m.