load_contig_lengths: Load a contig lengths file

In INRA-LPGP/PoolSex-vis: Visualization of results from PSASS

Description

Loads a table of contig lengths. The function separates the lengths of chromosomes and unplaced contigs If chromosomes names are provided, they will be used to determine the chromosomes. Otherwise, the function will attempt to detect chromosomes based on contig names (chromosomes start with LG / Chr / NC).

Usage

load_contig_lengths(
  input_file_path,
  chromosomes_names = NULL,
  plot.unplaced = TRUE
)

Arguments

input_file_path	Path to a contig lengths file.
chromosomes	A vector of chromosomes names obtained with the load_chromosomes_names function (default NULL).

Value

A list with the following elements: - lg : lengths of contigs determined to be chromosomes - unplaced : lengths of contigs determined to be unplaced - plot : lengths of sectors to be plotted

Examples

lengths <- load_contig_lengths("contig_lengths.tsv", chromosomes_names = chromosomes_names)

INRA-LPGP/PoolSex-vis documentation built on March 7, 2020, 6:03 p.m.