common_params: Function to hold common parameters.
In rpolicastro/tsrexplorer: TSS and TSR Analysis

Function to hold common parameters.

common_params(
  experiment,
  genome_assembly,
  genome_annotation,
  sample_sheet,
  threshold,
  samples,
  use_normalized,
  ncol,
  log2fc_cutoff,
  fdr_cutoff,
  dominant,
  exclude_antisense,
  data_conditions,
  rasterize,
  raster_dpi,
  return_table
)

`experiment`	TSRexploreR object.
`genome_assembly`	Genome assembly in FASTA or BSgenome format.
`genome_annotation`	Genome annotation in GTF, GFF3, or TxDb format.
`sample_sheet`	A sample sheet data.frame or tab delimited file. Must have the columns 'sample_name', 'file_1', and 'file_2'. Additional meta-data columns can be added with sample information such as condition and batch.
`threshold`	TSSs or TSRs with a score below this value will not be considered.
`samples`	A vector of sample names to analyze.
`use_normalized`	Whether to use the normalized (TRUE) or raw (FALSE) counts.
`ncol`	Integer specifying the number of columns to arrange multiple plots.
`log2fc_cutoff`	Differential features not meeting this \|log2(fold change)\| threshold will not be considered.
`fdr_cutoff`	Differential features not meeting this significance threshold will not be considered.
`dominant`	If TRUE, will only consider the highest-scoring TSS per gene, transcript, or TSR or highest-scoring TSR per gene or transcript.
`exclude_antisense`	Remove antisense TSSs/TSRs prior to analysis.
`data_conditions`	Apply advanced conditions to the data.
`rasterize`	Rasterize a ggplot.
`raster_dpi`	If rasterization is set, this controls the rasterization DPI.
`return_table`	Return a table of results instead of a plot.