set_par_list: S4 class of the parameter list
In jkruppa/virDisco: Modules for a viral detection pipeline

Description Usage Arguments Details Value Author(s)

Generates the S4 class of the parameter list

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set_par_list(index_genome_dir, index_amino_dir, qc = TRUE,
  set_mapper = "bowtie", ref_seq_file = "", prot_info_df = "",
  species_info_df = "")

`index_genome_dir`	path to the index of the reference genome generated by Bowtie2 or Star
`index_amino_dir`	path to the index of the amino acid reference genome generated by Pauda
`qc`	should the quality trimming used [true]
`set_mapper`	which mapper should be used [bowtie]
`ref_seq_file`	path to the reference sequence file in fasta format
`prot_info_df`	sqlite3 database of the protein information, see `setup_aa_info_sample_sqlite` for setup
`species_info_df`	sqlite3 database of the species/strain information, see `setup_species_info_sqlite` for setup

The S4 class has some validity functions to check the input parameters. The access of the functions always runs by par_list["value"]. If no S4 class is wanted, the user could also build a own list object with the given names.

A S4 class with the following slots [default values]

num_decoy_reads = "numeric": number of generated decoy reads, if decoy is true [500]
min_num_reads = "numeric": mimimum number of reads per reference [50]
min_coverage = "numeric": mimimum coverage of the reference by reads to keep the hit [0.05]
map_dna_in = "list": internal file storage for dna mapping
map_dna_stats = "list": internal list for DNA mapping statistics
map_pep_in = "list": internal file storage for amino mapping
decoy = "logical": should the decoy approach be run [false]
tax = "logical": should the tax trees are generated [true]
qc = "logical": should the quality control by trimmomatic be run [true]
clean = "logical": should intermediate files be deleted [true]
paired = "logical": should paired read infiles assumed [false], but will be checked internally
plot = "logical": should the final visualization of the mapped reads plotted [true]
black_list = "character": list of corrupt NCBI GenBAnk IDs [Null]
gen_prot_sep = "character": the seperator, how the genebank_id is seperated prom the prot_id [_]
check_host = "logical": should the host be checked by blastn [true]
run_dna_mapping = "logical": should the DNA mapping be run [true]
run_pep_mapping = "logical": should the amino acid mapping be run? [true]
consensus = "logical": should the consensus of the reads be generated [true]
tmp_dir = "character": path to the temp dir [/home/temp]
sql_dir = "character": path to the sql dir [/home/sql]
index_genome_dir = "character": path to the genome index generated by Star or Bowtie2
index_amino_dir = "character": path to the amino index generated by Pauda
ref_seq_file = "character": path to the reference.fasta
prot_info = "tbl_dbi": sqlite3 database of the protein information
species_info = "tbl_dbi": sqlite3 database of the species/strain information
plot_id = "character": should only a subset of genebank_ids be plotted?
mapper = "character": sould the Bowtie2 or Star mapper be used [bowtie]
num_plot = "numeric": how many plots of the TOP'num_plot' should be generated [25]
ncore = "numeric": how many cores should be used
pdf_file = "character": name of the final plot pdf file