Man pages for jngwehi/loxcodeR
Loxcode Tools
| data | Access decoded cassette data |
| decode | Decode FASTQ |
| decode_output-class | S4 class to contain output of decode() |
| dist_count_beeswarm_plot | Show recombination distance distribution by size as beeswarm... |
| dist_orig_plot | Plots distribution of dist_orig found in sample |
| get_cass_vec | Convert vector of cassette strings to list of numeric vectors |
| get_data | Get unvalidated readout data for a given sample |
| get_origin_dist | Fetch distances from origin (dist_orig) |
| get_pair_dist | Get pairwise distance |
| get_rec_prob | Get recombination distance distribution |
| get_valid | Get validated readout data for a given sample |
| heatmap_plot | Generate heatmap from count_matrix (TW/31/10/2019) |
| impute_13 | Impute missing elements |
| impute_13_impl | Impute missing element in a 13-element cassette |
| impute-loxcode_sample-method | Impute missing code in 13-element cassettes |
| is_valid | Check if cassette is valid |
| load_from_xlsx | Create experiment |
| load_origin_distmaps | Load distance maps for distance-to-origin |
| load_pair_distmaps | Load distance maps for pairwise distances |
| load_prob_files | Load probability tables (Markov chain) |
| load_samples | Load data from FASTQ for all samples in a loxcode_experiment... |
| loxcode_experiment-class | Loxcode experiment object |
| loxcode_sample-class | S4 class to represent loxcode experimental sample data |
| makeid | Get cassette IDs |
| merge_by | Merge samples by label |
| merge_sample | Merge two loxcode_sample objects |
| name | Fetch experiment name |
| name-set | Set experiment name |
| pack | Pack cassettes into cassette ID |
| pair_comparison_plot | Produce pair comparison scatterplot |
| rank_count_plot | Produce rank-count plot |
| readstats_plot | Read stats (TW/01/11/2019) |
| retrieve_dist_origin_single | Assumes that input cassette is valid already! |
| retrieve_prob_ensemble | Get ensemble generation probability |
| run_markov | Calculate generation probabilities using Markov chain... |
| sample | Get loxcode_sample object by sample name |
| sample_comparison_pie | sample comparison pie (TW/05/11/2019) |
| sampnames | Fetch names of samples |
| sampnames-set | Set names of samples |
| samptable | Get sample table |
| samptable-set | Set sample table |
| setup_count_matrix_codesets | Generate count_matrix from individual samples and add... |
| size_plot | Plots distribution of loxcode sizes found in sample |
| summary_table | summary table |
| valid | Access decoded cassette data, valid cassettes only |
| validate-loxcode_sample-method | Add cassette validation column to decoded cassette data |
| venn_2way | 2-way Venn diagram |
| venn_3way | 3-way Venn diagram |
