Man pages for EvolEcolGroup/mtDNAcombine
R package to download, combine, and curate sequences from public databases
| align_and_summarise | Aligns sequence data, plots haplotype networks and summarises... |
| build_genbank_df | Builds a reference data frame with details of all available... |
| check_poss_synyms | Checks if scientific name for sample is likely a species, or... |
| drop_low_haplo_number | Drops populations from main data frame when haplotype number... |
| drop_low_sample_size | Drops populations from main data frame when sample size is... |
| drop_low_sequence_length | Drops populations from main data frame when sequence length... |
| export_details | Exports downloaded details into seperate .csv files for each... |
| export_sequences | Exports downloaded details into seperate .csv files for each... |
| gene_of_interest | Extracts data frame rows associated with a specified gene of... |
| get_GB_sequence_data | Builds a curated data frame with sample details and sequence... |
| get_gene_details | Gets details of all available genes associated with accession... |
| get_sample_details | Gets details of individual samples |
| hapfreq_from_paper | Find instances where all accessions from one paper are unique... |
| identify_outlier | Identifies original accession number of given haplotype index... |
| load_accession_list | Loads list of accession numbers |
| magnify_to_sampled_freq | Multiplies sequence data up to sampled frequency, aligns and... |
| outliers_dropped | Identifies original accession number of given haplotype index... |
| remove_duplicates | Removes multiple copies of one gene |
| setup_basic_xml | Creates basic skeleton xml files |
| standardise_gene_names | Standardises the range of gene names used in GenBank |
| standardise_spp_names | Updates any species names user wants to alter |
| updating_info_df | Multiplies sequence data up to sampled frequency, aligns and... |
