Perform Fisher test overrepresentation analysis of each subgroup — runFISHERmods • K2Taxonomer

Adds overrepresentation testing results using the output of runDGEmods().

Usage

runFISHERmods(
  K2res,
  genesets = NULL,
  qthresh = NULL,
  cthresh = NULL,
  ntotal = NULL
)

Arguments

genesets: Named list. Feature sets to be includes in enrichment-based analyses.
qthresh: Numeric. A value between 0 and 1 indicating the FDR cuttoff to define feature sets.
cthresh: Numeric. A positive value for the coefficient cuttoff to define feature sets.
ntotal: Numeric. A positive value to use as the background feature count. 20000 by default.

Value

An object of class K2.

References

Reed ER, Monti S (2021). “Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.” Nucleic Acids Research. doi:10.1093/nar/gkab552 , https://pubmed.ncbi.nlm.nih.gov/34226941/. Benjamini Y, Hochberg Y (1995). “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289--300. ISSN 00359246, doi:10.1111/j.2517-6161.1995.tb02031.x , http://doi.wiley.com/10.1111/j.2517-6161.1995.tb02031.x.