A small example of the analytical datasets created by ogrdbstats from repertoires and reference sets. The dataset can be created by running the example shown for the function read_input_data(). The dataset is created from example files provided with the package. The repertoire data is taken from Rubelt et al. 2016, <doi: 10.1038/ncomms11112>
example_rep## `example_rep` - a named list containing the following elements:
| ref_genes | named list of IMGT-gapped reference genes |
| inferred_seqs | named list of IMGT-gapped inferred (novel) sequences. |
| input_sequences | data frame with one row per annotated read, with CHANGEO-style column names. The column SEG_CALL is the gene call for the segment under analysis. Hence if segment is 'V', 'V_CALL' will be renamed 'SEG_CALL' whereas is segment is 'J', 'J_CALL' is renamed 'SEG_CALL'. This simplifies downstream processing. Rows in the input file with ambiguous SEG_CALLs, or no call, are removed. |
| genotype_db | named list of gene sequences referenced in the annotated reads (both reference and novel sequences) |
| haplo_details | data used for haplotype analysis, showing allelic ratios calculated with various potential haplotyping genes |
| genotype | data frame containing information provided in the OGRDB genotype csv file |
| calculated_NC | a boolean that is TRUE if mutation counts were calculated by this library, FALSE if they were read from the annotated read file |