Man pages for ShawHahnLab/microsat
Computational, High-throughput Individual Identification through Microsatellite Profiling
| align_alleles | Align allele sequences across loci |
| allele_match | Check Sample Data for Potential Allele Matches |
| analyze_dataset | Analyze all samples in a dataset |
| analyze_sample | Analyze sequence table and categorize sequences |
| analyze_seqs | Analyze a set of STR sequences |
| apply_config | Apply CHIIMP options globally |
| calc_genotype_distance | Calculate distance between two genotypes |
| categorize_genotype_results | Categorize genotyping results |
| cfg | Get/set CHIIMP global configuration options |
| CFG_DEFAULTS | Default Configuration |
| check_length | Check sequences for expected length |
| check_motif | Check sequences for STR repeats |
| chiimp-package | CHIIMP |
| CMP | Complements of IUPAC nucleotide codes |
| find_artifact | Check for non-stutter PCR artifacts between sequences |
| find_closest_matches | Find closest matches in distance matrix |
| find_primer_matches | Find primer matches for reads |
| find_stutter | Check for PCR stutter between sequences |
| format_pandoc_args | Create Pandoc Metadata Argument Strings |
| full_analysis | Perform a full microsatellite analysis |
| get_px_width | Get plot unit width |
| handle_primers | Modify reads based on matched primers |
| histogram | Plot histogram of STR sequences |
| load_allele_names | Load table of known allele names |
| load_config | Load configuration file |
| load_config_csv | Load configuration file from CSV |
| load_config_yaml | Load configuration file from YAML |
| load_csv | Load and save tables from CSV |
| load_dataset | Load table of sample attributes |
| load_genotypes | Load table of genotypes |
| load_locus_attrs | Load table of locus attributes |
| load_seqs | Load vector of sequences from FASTA/FASTQ file |
| logmsg | Write Log Message |
| main | Handle full microsatellite analysis from command-line |
| make_allele_names | Create Short Allele Names |
| make_dist_mat | Make distance matrix for set of samples |
| make_dist_mat_known | Make distance matrix for samples to known genotypes |
| make_entry_id | Create identifiers for STR Data |
| make_raw_nt | Make matrix of raw bytes from nucleotide sequences |
| make_read_primer_table | Make data frame of primer info for reads |
| make_rownames | Create Row Names for STR Data |
| match_known_genotypes | Associate known genotypes with samples |
| name_alleles_in_table | Name allele sequences in genotype data frame |
| name_known_sequences | Name known allele sequences |
| order_entries | Define Ordering for STR Data |
| parse_config | Parse a configuration data frame into list |
| plot_alignment | Plot Sequence Alignments |
| plot_cts_per_locus | Plot heatmap of read counts matching each locus primer |
| plot_dist_mat | Plot Distance Matrix |
| plot_heatmap | Render heatmap of STR attribute across samples and loci |
| plot_heatmap_artifacts | Plot heatmap of suspected PCR artifacts |
| plot_heatmap_homozygous | Plot heatmap of homozygous samples |
| plot_heatmap_prominent_seqs | Plot heatmap of samples with multiple prominent sequences |
| plot_heatmap_proportions | Plot heatmap of proportion of allele sequence counts |
| plot_heatmap_stutter | Plot heatmap of suspected PCR stutter |
| prepare_dataset | Extract Sample Attributes from Filenames |
| RAW_NT | IUPAC DNA nucleotides as raw bytes |
| remove_shared_root_dir | Remove shared path from file paths |
| render_report | Render Microsatellite Report Document |
| report_genotypes | Create genotype summary table |
| report_idents | Create identification summary table |
| revcmp | Reverse complement sequences |
| sample_analysis_funcs | Versions of analyze_sample |
| sample_summary_funcs | Versions of summarize_sample |
| save_alignment_images | Save alignment visualizations to image files |
| save_alignments | Save alignments to FASTA files |
| save_allele_seqs | Save identified alleles to FASTA files |
| save_data | Save Microsatellite Analysis to Disk |
| save_dataset | Save table of sample attributes |
| save_dist_mat | Save sample distance matrix to text file |
| save_histograms | Save sequence histogram visualizations to image files |
| save_results_summary | Save dataset summary to text file |
| save_sample_data | Save per-sample processed data to text files |
| save_seqfile_data | Save per-file processed data to text files |
| setup_package | Set up CHIIMP package environment |
| sort_results | Sort entries in results data frames |
| str_hist_render | Draw prepared histogram data |
| str_hist_setup | Prepare histogram data |
| str_hist_setup_legend | Setup display attributes for STR histogram |
| summarize_attribute | Create Summary Attribute Table |
| summarize_dataset | Add further summaries to analyzed dataset |
| summarize_genotypes | Create Summary Genotype Table |
| summarize_genotypes_known | Create Summary Genotype Table for Known Genotypes |
| summarize_sample | Summarize a processed STR sample |
| tabulate_allele_names | Wide table of allele names vs loci |
| tally_cts_per_locus | Create Counts-per-Locus Table |
| test_data | Helper Data for Examples |
| tidy_analyzed_dataset | Tidy raw analyzed dataset results |
| version_compare | Compare two version strings |
