load_data_files: Load a single data file

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

Description

Loads all data files from PSASS and other files needed for the plots.

Usage

load_data_files(
  contig_lengths_file_path,
  prefix = NULL,
  window_fst_file_path = NULL,
  position_fst_file_path = NULL,
  window_snps_file_path = NULL,
  position_snps_file_path = NULL,
  depth_file_path = NULL,
  chromosomes_names_file_path = NULL,
  plot.unplaced = TRUE
)

Arguments

contig_lengths_file_path	Path to a contig lengths file.
prefix	Prefix (including full path) to a complete dataset. If prefix is specified, it will be override individual file specifications such as "window_fst_file_path" (default NULL).
window_fst_file_path	Path to a FST window output file (default NULL).
position_fst_file_path	Path to a FST positions output file (default NULL).
window_snps_file_path	Path to a SNPs window output file (default NULL).
position_snps_file_path	Path to a SNPs positions output file (default NULL).
depth_file_path	Path to a depth output file (default NULL).
chromosomes_names_file_path	Path to a contig names file (default NULL).
plot.unplaced	If TRUE, unplaced contigs will be plotted as a supercontig (default TRUE).

Value

A list with the following elements: - names : chromosomes names (if specified) - lengths : contig lengths - window_fst : sliding window fst data (if specified) - position_fst : position fst data (if specified) - window_snp : sliding window snp data (if specified) - position_snp : position snp data (if specified) - depth : depth data (if specified)

Examples

data <- load_data_files(prefix = "data/poolseq_analysis", chromosomes_names_file_path = "data/chromosomes_names.tsv",
                        contig_lengths_file_path = "data/contig_lengths.tsv")

data <- load_data_files(window_fst_file_path = "data/poolseq_analysis_window_fst.tsv",
                        window_snps_file_path = "data/poolseq_analysis_window_snps.tsv",
                        depth_file_path = "data/poolseq_analysis_depth.tsv",
                        contig_lengths_file_path = "data/contig_lengths.tsv",
                        plot.unplaced = FALSE)

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