set_settings: Set Settings.
In rpolicastro/ZentTools: What the Package Does (One Line, Title Case)

Set Settings.

set_settings(
  zent_obj,
  analysis_type = NA,
  paired = NA,
  ncores = NA,
  genome_dir = NA,
  genome_annotation = NA,
  genome_assembly = NA,
  alignment_dir = NA,
  peak_dir = NA
)

`zent_obj`	ZentTools object.
`analysis_type`	Type of experiment. Either 'RNA-seq', 'ChIP-seq', or 'ChEC-seq'.
`paired`	Paired-end status of the reads. Either TRUE or FALSE.
`ncores`	The number of cores/threads to use.
`genome_dir`	The directory of the genome index.
`genome_annotation`	The directory and file name of the the genome index GTF file.
`genome_assembly`	The directory and file name of the the gnome assembly FASTA file.
`alignment_dir`	The directory containing the aligned reads.
`peak_dir`	The directory containing the called peaks.