Man pages for jkruppa/viralDetectTools
Modules for a viral detection pipeline
| aa_info_db | Example amino acid information db |
| aa_seqs | AAStringSet of amino acid sequences |
| artificial_genome_mapping | Control function for the artificial mapping |
| build_index | Build a index for DNA and AA mapper |
| build_sample_info | Internal function to extract the sample information |
| check_host | Experimental function to check the host by blastn |
| collapse_df | Collapse a matrix by row |
| coverage_filter | Filter the hits by the coverage |
| dna_seqs | DNAStringSet of DNA sequences |
| empty_map_pep_list | Internal empty object for pepe mapping |
| ete2_plot | Control function for the ete3 phylogenetic trees |
| fastq_quality_control | Main fastq quality function |
| fastq_trimmer | Internal trimmomatic call function |
| fq2fa | A wrapper for seqtk to convert fastq to fasta |
| generate_decoy_reads | Generates (decoy) reads from a sequence |
| generate_read | Generates a _single_ read from a sequence |
| get_bowtie2_cmd | Wrapper to build up the Bowtie2 command |
| get_consensus_df | Get the consenus sequence of the read hits to the reference |
| get_pauda_hits | Internal parse function for PAUDA |
| get_seq_chunks_by_threshold | Divide sequences into chunks |
| get_sub_files | Gather the files for one sample run |
| infected_fastq | Example fastq files |
| is.named | Small tester if a object is named |
| map_dna_ref | DNA mapping function |
| map_pep_ref | Amino mapping function |
| mapping_dna_plot | Mapping the viral read hits to the reference |
| NHS_10001_consensus | Output of get_consensus_df |
| NHS_10001_count_tbl | Output of ord_findings |
| NHS_10001_map_aa_list | Output of map_pep_ref |
| NHS_10001_map_dna_list | Output of map_dna_ref |
| ord_findings | Order the hits of the mapping |
| plot_time_sample | Plot the processed files in a dir |
| prepare_file_list | Get all the files prepared in a directory |
| random_dna_seq | Shuffle a sequence with a kept kmer distribution |
| run_batch_job | Function to run the pipeline on one folder |
| sam2bam_serial | Wrapper function for samtools |
| set_par_list | S4 class of the parameter list |
| set_program_list | Path to the external program executables |
| setup_aa_info_sample_sqlite | Function to build up the aa_info_sample_sqlite database |
| setup_aa_info_sqlite | Function to build up the aa_info_sqlite database |
| setup_species_info_sqlite | Function to build up the species_info_sqlite database |
| strain_info_db | Example species infro db |
| talk | Advanced message functionality by time stamp |
| tbl_sqlite_check | Test function to check the sqlite2 databases for consistency |
| TIME | Small wrapper to extract the time from Sys.time() |
