LACEinterface: LACE interface

### info_help.R --
###
### Help strings for various bits and pieces of the LACE GUI.
###
### See file LICENSE in the main folder for licensing and copyright
### information.

text = list()

text[["pr_name"]] =
    "Give a name to your project\'s experiment. All the results will be stored inside a subfolder with the same name."

text[["pr_folder"]] =
    "Select a folder to store the the project. Path containing project is recognized and saved state is reloaded."

text[["sc_metadata_file"]] =
    "Select file containing at least two columns, one with cell ids (such that id.vcf and id.bam identify the respective files) and the other with the sampling times (\'before drag\', etc.). Accepted file formats are csv and tsv, or rds containg a data.frame object. Headers are required. The list can contains more cells than what are stored in HD."

text[["m_idCol"]] =
    "Select the column containing cell ids. (such that id.vcf and id.bam identify the respective files)"

text[["m_timePointsCol"]] =
    "Select the column containing the sampling times. Sampling time tags can concide with the ids if the case."

text[["m_timePoints"]] =
    "Select and drag one or more sampling points to order them chronologically."

text[["m_doSave"]] =
    "Alpha release: Save state for the current tab."

text[["m_doLoad"]] =
    "Alpha release: Load state for the current tab. Inconguencies are reported (you messed with the config files)."

text[["av_exec"]] =
    "Alpha release: Run current part of the pipeline (in the last tab run the whole pipeline [alpha: did u test it before releasing it?])."

text[["av_anovar_exec_dir"]] =
    'Folder containing the Annovar executables. Annovar is available at this <a href="https://annovar.openbioinformatics.org/en/latest/user-guide/download/">link</a>.'

text[["av_anovar_db_dir"]] =
    "Annovar requires a database with annotations.
     Some are distributed with the software. Refer to the website guide to create your own database of annotated variants."

text[["av_vcf_in_dir"]] =
    "This is the folder where variant calling files are stored.
     File names need to have the format ID.vcf, where ID belongs to the metadata list, otherwise the file is neglected."

text[["thr_maf"]] =
    "Minor allele frequency (MAF) for each referenced SNP included in a default global population, ranging from <1 to <50%.
MAF is a ratio defined as
$MAF={Alleles positive for the variant}/{Total alleles screened}$ . When there are more than two alleles at a variant location, the second most frequent is used to calculate MAF."

text[["thr_alleles_ratio"]] =
    "Alternate allele frequency is the ratio of the obseved alterative allele and total obervations at that locus in a cell."

text[["thr_freq"]] =
    "How frequent is a variant found in a sample. It represents the ratio of cells where the mutation was observed over the total number of cells at a specific sampling time."

text[["thr_bucket_var_list"]] =
    "Table with functions"

text[["dp_samtools_exec_dir"]] =
    'Folder containing the Samtools suit executables. Samtools is available at this <a href="https://www.htslib.org/">link</a>.'

text[["dp_bam_dir"]] =
    "This is the folder where Binary Alignment Map files are stored.
File names need to have the format ID.bam, where ID is in the metadata list, otherwise the file is neglected."

text[["va_depth_minimum"]] =
    "Minimum depth to set values to NA."

text[["va_missing_values_max"]] =
    "Maximum number of considered missing data per gene."

text[["va_minumum_median_total"]] =
    "Minimum median depth for total reads."

text[["va_minumum_median_mutation"]] =
    "Minimum median depth for reads supporting mutations."

text[["va_verified_genes"]] =
    "Depending on the experiment, some genes may be more relevant than others.
The list of available genes changes based on the above filters.
Leave empty to consider all the vailable genes."

text[["inf_learning_rate"]] =
    "Parameter to tune the probability of accepting solutions at lower values during mcmc. Value of learning_rate = 1 (default), set a probability proportional to the difference in likelihood; values of learning_rate greater than 1 inclease the chance of accepting solutions at lower likelihood during mcmc while values lower than 1 decrease such probability."

text[["inf_alpha"]] =
    "False positive error rate provided as list of elements; if a vector of alpha (and beta) is provided, the inference is performed for multiple values and the solution at maximum-likelihood is returned."

text[["inf_beta"]] =
    "False negative error rate provided as list of elements; if a vector of beta (and alpha) is provided, the inference is performed for multiple values and the solution at maximum-likelihood is returned."

text[["inf_num_iter"]] =
    "Maximum number of mcmc steps to be performed during the inference."

text[["inf_num_rs"]] =
    "Number of restarts during mcmc inference."

text[["inf_n_try_bs"]] =
    "Number of steps without change in likelihood of best solution after which to stop the mcmc."

text[["inf_num_processes"]] =
    "Number of processes to be used during parallel execution. To execute in single process mode, this parameter needs to be set to either NA or NULL."

text[["inf_seed"]] =
    "Seed for reproducibility."

text[["inf_random_tree"]] =
    "Boolean. Shall I start MCMC search from a random tree? If FALSE (default) and initialization is NULL, search is started from a TRaIT tree (BMC Bioinformatics . 2019 Apr 25;20(1):210. doi: 10.1186/s12859-019-2795-4)."

text[["inf_marginalize"]] =
    "Boolean. If true, the attachment of cells to clones matrix is marginalized when computing likelihood."

text[["inf_keep_equivalent"]] =
    "Boolean. If true, results (the maximum likelihood longitudinal clonal tree, the attachment of cells to clones matrix) at equivalent likelihood with the best returned solution are returned."

text[["inf_check_indistinguishable"]] =
    "Boolean. If true, any indistinguishable event is removed from input data prior inference."

text[["inf_error_move"]] =
    "Boolean. If true, estimation of error rates in the MCMC moves is included."

text[["inf_show"]] =
    "Boolean. Show the interactive interface to explore the output."


### end of file -- info_help.R