set_settings: Set Settings.
In Bankso/SCAR: SpLiT-ChEC analysis with R

set_settings

R Documentation

Set Settings.

Description

Set Settings.

Usage

set_settings(
  SCAR_obj,
  analysis_type = NA,
  paired = NA,
  ncores = NA,
  genome_dir = NA,
  genome_index = NA,
  genome_assembly = NA,
  alignment_dir = NA,
  peak_dir = NA,
  compare = NA,
  plot_dir = NA,
  comp_op = NA
)

Arguments

`SCAR_obj`	SCAR object, holds data for use in all the functions.
`analysis_type`	Type of experiment. 'ChIP-seq', 'ChEC-seq', or 'SChEC-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_index`	The location of the bowtie2 genome index
`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.
`compare`	For deeptools, do you want to use bamCompare?
`plot_dir`	directory for plotting outputs
`comp_op`	Single operation for comparison of coverage