common_params: Function to hold common parameters.

In zentnerlab/TSRexploreR: TSS and TSR Analysis

Function to hold common parameters.

Description

Function to hold common parameters.

Usage

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
)

Arguments

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.

zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.