Description Usage Arguments Details Value Author(s)
Generates the S4 class of the parameter list
1 2 3 | 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 |
species_info_df |
sqlite3 database of the species/strain
information, see |
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]
number of generated decoy reads, if decoy is true [500]
mimimum number of reads per reference [50]
mimimum coverage of the reference by reads to keep the hit [0.05]
internal file storage for dna mapping
internal list for DNA mapping statistics
internal file storage for amino mapping
should the decoy approach be run [false]
should the tax trees are generated [true]
should the quality control by trimmomatic be run [true]
should intermediate files be deleted [true]
should paired read infiles assumed [false], but will be checked internally
should the final visualization of the mapped reads plotted [true]
list of corrupt NCBI GenBAnk IDs [Null]
the seperator, how the genebank_id is seperated prom the prot_id [_]
should the host be checked by blastn [true]
should the DNA mapping be run [true]
should the amino acid mapping be run? [true]
should the consensus of the reads be generated [true]
path to the temp dir [/home/temp]
path to the sql dir [/home/sql]
path to the genome index generated by Star or Bowtie2
path to the amino index generated by Pauda
path to the reference.fasta
sqlite3 database of the protein information
sqlite3 database of the species/strain information
should only a subset of genebank_ids be plotted?
sould the Bowtie2 or Star mapper be used [bowtie]
how many plots of the TOP'num_plot' should be generated [25]
how many cores should be used
name of the final plot pdf file
Jochen Kruppa
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