Release v1.3.0 · sof202/ChromOptimise

Features

Added usage to main script that shows if called incorrectly
Added a supplementary script to recreate transitions matrices without main diagonal, increasing interpretability (#36)
Made a colour blind friendly (and more easily interpretable) colour scheme for heritability heatmaps (#38)
Added an option to customise the ldsc window size, helps with model misspecification (#39)
Added a check to see if all states in smaller models are indeed in the 'optimum model' for further validation (#40)
Added a check that warns the user if the optimum model has a larger BIC than a smaller model (unlikely to occur in my experience)
Added another point to the redundant states criterion. States are expected to have a certain level of 'stability' which is now also measured via calculating the expected number of contiguous state assignments for each state. Low contiguity being associated with instability (#41)

Revamp the way software is used in ChromOptimise
- Conda is now used to obtain R, Java openjdk and bedtools (#44)
- renv is now used to obtain the necessary R packages/libraries (#46)

Now selects a single state assignments file if multiple cell types were used in training
Various X11 issues on remote servers
Warning message for heritability plot is written to correct output directory
Force use of Cairo for image generation
Correctly output the number of states in optimum model for the rest of the pipeline to use in the case where the largest model is considered optimal.
Add execution permissions to all Rscripts to avoid file permission errors with SLURM on some systems

use [[""]] notation for extraction in Rscripts
Use seq_along and seq_len over 1:nrow() where possible
Favour the usage of dplyr package where possible (also results in performance increases in some areas)
Removal of setwd()
Use of file.path for more portable file paths (though it is expected that scripts are ran on Linux systems still)
Prefer the usage of .tsv files over .csv files.
Remove filenames from scripts in favour of basename $0, this reduces misleading incorrect file names (#42)

Added redirection to wiki page to give suggestions on max wall times
Updated software requirements and dependencies (for individual scripts)
Fixed some broken mathematical equations (not rendering correctly)
Added explanation behind colour scheme seen in heritability heatmap plots (#38)
Removed duplication of information in preambles (usage has same info)
Fix the ordering of sidebars to reflect importance and ordering of pipeline scripts