Man pages for TransmissibleCancerGroup/dftdLowCov
| chrom_ranges_from_lengths | Calculate chromosome ranges from chromosome lengths |
| clade_colours | Generate a colour palette for the DFT1 clades |
| coverage_depth_summary | Counts the number of bases covered by 0, 1, 2 etc CNV... |
| coverage_histogram | Calculates the depth at |
| depth_of_coverage | Calculates the depth of coverage (of CNV segments) for the... |
| do_simulation | Simulation code |
| get_aberrant_copy_number_per_sample | Make a table of aberrant copy number states for each... |
| get_depth | Calculate number of bases covered by a table of CNVs Start... |
| hello | Hello, World! |
| isCarcinoma | Return a vector of carcinoma-specific CNV IDs |
| isCellLine | Return a vector of CNV IDs for cell line samples |
| isDFT1 | Return a vector of CNV IDs for DFT1 samples |
| isDFT2 | Return a vector of CNV IDs for DFT2 samples |
| isMultiGain | Return a vector of CNV IDs associated with a copy number gain... |
| isMultiLoss | Return a vector of CNV IDs associated with a copy number loss... |
| isNonDFTD | Return a vector of CNV IDs for non-DFTD samples |
| is.overlap | Returns TRUE if vectors a and b overlap |
| is_variant_site | Check if a vector of characters is a variant site |
| load_chromosome_lengths | load_chromosome lengths into a list |
| load_cnv_table | Loads the CNV table (supplementary table S3) in data.table... |
| load_sample_table | Loads the tumour sample table (supplementary table S1A) in... |
| make_coordinates | Helper for making matching segment tables when looking at... |
| make_presence_absence_table | Make a presence / absence table for CNVs Melts the CNV table... |
| pad | Pad vector v to length padlen, using padval as the added... |
| parse_aberrant_copy_number_states | parse_aberrant_copy_number_states |
| parse_sample_cnv_group | parse_sample_cnv_group |
| parse_sample_cnv_group_and_count | parse sample cnv group and count |
| parse_sample_cnv_group_with_clade | parse_sample_cnv_group_with_clade Also capture the clade... |
| plot_chromosome_map | Plot an individual chromosome's map. Assumes dt.gains and... |
| preprocess_for_simulation | Data cleaning ready for making simulations |
| randomize_positions_over_whole_genome | Takes a data frame of segments and randomises their start... |
| rectangle_packing | Algorithm to pack segments into layers for plotting. Greedily... |
| rectangle_packing2 | Algorithm to pack segments into layers for plotting. Greedily... |
| rectangle_packing3 | A faster algorithm to pack aligned reads into layers |
| rectangle_packing4 | A faster algorithm to pack aligned reads into layers. Doesn't... |
| scan_col | Easier extraction of data from data table columns using regex |
| split_chars | Split a string into a vector of component characters |
| wrap_around | Wrap segments that exceed the limit value back into the start... |
| write_fasta | Write sequence information in a table to FASTA format |
