load_mapping_results: Load a mapping results file

In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

Description

Loads a table of mapping results obtained with the RADSex mapping module.

Usage

load_mapping_results(input_file_path, contig_lengths_file_path,
  contig_names_file_path = NULL, plot.unplaced = TRUE)

Arguments

input_file_path	Path to a mapping results file from RADSex map.
contig_lengths_file_path	Path to a contig lengths file from RADSex map.
contig_names_file_path	Path to a file containing the chromosomes names.
plot.unplaced	If TRUE, unplaced scaffolds will be grouped together and plotted as "Unplaced" (default: TRUE).

Value

A list with the following elements:

data	A data frame of the mapping results.
lengths	The contig lengths.
names	A vector with reference contigs names as names and corresponding contig names as values

Examples

data <- load_mapping_results("mapping_results.tsv", contig_lengths_file_path = 'contig_lengths.tsv',
                             contig_names_file_path = 'contig_names.tsv')

RomainFeron/radsex-vis documentation built on May 23, 2019, 2:48 p.m.