Man pages for philliplab/MotifBinner
Bin reads by Motif
| add_snps | Adds n snps to each sequence in seq_dat |
| align_sequences | A wrapper for a number of alignment tools |
| bin_by_name | Groups sequences together into bins based on their names |
| bin_file | Bins a given FASTA file and outputs each bin as a seperate... |
| check_classification | Checks that the output from a classifier satisfies basic... |
| classify_absolute | Removes the most outlying sequences in a bin until the... |
| classify_bin | Classify a bin's sequences into 'src' and 'out' |
| classify_bin_infovar_balance | Finds the outliers in a bin by balancing the amount of... |
| classify_bin_most_frequent | Classifies the sequences in a set by only choosing the most... |
| classify_bin_random | Randomly classify a number of unique sequences to the 'out'... |
| clean_matches | Internal Function: Clean matches to the motifs |
| clean_seq_data | Internal Function: Clean sequence data for motif extraction |
| compare_dists | Compare two distance matrices. |
| construct_consensus | Constructs a consensus string using the specified technique |
| create_scenario_data | Compute the scenarios that are not already in the scenario... |
| dput_classified_binned_folder | Reads in all files from a folder, assuming that they are... |
| extract_motifs | Extracts motifs from a set of reads |
| extract_motifs_iterative | A wrapper for extract motifs parallel that will iteratively... |
| extract_motifs_par | A wrapper for extract motifs that will execute it in a... |
| fast_stringDist | Computes a distance matrix between sequences by using... |
| file_to_consensus | Bins and constructs consensus sequences for an entire fastq... |
| gen_and_contaminate_reads | Generate contaminated reads |
| gen_error_profile | Generates a read error profile |
| gen_error_profile_uniform | Generates a read error profile by assigning a constant... |
| gen_pid_search_scenario | Simulate a scenario that can be used to test PID detection |
| gen_reads | Generates a specified number of reads from a given sequence... |
| gen_seq | Simulates a random sequence of a given length |
| get_mislabel_test_data | Returns that dataset used for testing the mislabel detection |
| get_test_settings | Provides some settings useful for testing |
| list_unique_scenarios | Given all the test cases list the unique scenarios |
| load_or_initialize_cache | Given the location of a cache file, intialize the cache |
| mostConsensusString | A custom consensus string constructor that just uses the... |
| muscle_par | Copy of muscle function from ape package with tweaks to allow... |
| mutate_base | Mutates a single base to another base |
| process_bin | Given a groups of sequences that were binned together, throw... |
| process_file | Processes a file into consensus bins |
| randomize_ambig | Removes ambiguous letters from a sequence by replacing them... |
| randomize_list | Randomizes the order of the items of a list |
| read_classified_binned_file | Reads a classified binned file and splits it into bins |
| read_sequence_file | Reads in a sequence file given a file name. |
| remove_motifs | Internal Function: Removes motifs from sequences given match... |
| run_all_tests | Runs all the tests |
| run_test | Run a test case |
| save_bin_report | Given a report_dat data list, generate and save the... |
| save_bin_results | Given a report_dat data list, save the important results into... |
| score_all_classifications | Given a list of datasets and a classification strategy, apply... |
| score_classification | Given a test dataset and a classification strategy, apply the... |
| score_consensus | Given a test bin of sequences, benchmark how well the input... |
| twoStepConsensusString | A custom consensus string constructor that uses a two step... |
