check_args_for_bootstrap_plot_generation: check_args_for_bootstrap_plot_generation

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

check_args_for_bootstrap_plot_generation

Description

Check the input arguments of the generate_bootstrap_plots_for_transcriptome.

Usage

check_args_for_bootstrap_plot_generation(
  sct_data,
  tt,
  thresh,
  annotLevel,
  reps,
  full_results,
  listFileName,
  showGNameThresh,
  sortBy
)

Arguments

sct_data	List generated using generate_celltype_data.
tt	Differential expression table. Can be output of topTable function. Minimum requirement is that one column stores a metric of increased/decreased expression (i.e. log fold change, t-statistic for differential expression etc) and another contains gene symbols.
thresh	The number of up- and down- regulated genes to be included in each analysis (Default: 250).
annotLevel	An integer indicating which level of sct_data to analyse (Default: 1).
reps	Number of random gene lists to generate (Default: 100, but should be >=10,000 for publication-quality results).
full_results	The full output of ewce_expression_data for the same gene list.
listFileName	String used as the root for files saved using this function.
showGNameThresh	Integer. If a gene has over X percent of it's expression proportion in a cell type, then list the gene name.
sortBy	Column name of metric in tt which should be used to sort up- from down- regulated genes (Default: "t").

Value

Null output.

NathanSkene/EWCE documentation built on April 30, 2024, 5:21 p.m.