Description Usage Arguments Value Examples
View source: R/load_data_files.R
Loads all data files from PSASS and other files needed for the plots.
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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). |
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)
1 2 3 4 5 6 7 8 | 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)
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