enrichMiR: enrichMiR

In ETHZ-INS/enrichMiR: enrichMiR: miRNA target enrichment analysis

enrichMiR

Description

A miRNA wrapper around 'testEnrichment', for continuity with previous enrichMiR versions. It is recommended to use testEnrichment instead.

Usage

enrichMiR(
  DEA,
  TS,
  miRNA.expression = NULL,
  families = NULL,
  cleanNames = FALSE,
  ...
)

Arguments

DEA	A data.frame of the results of a differential expression analysis, with features (e.g. genes) as row names and with at least the following columns: 'logFC', 'FDR'
TS	A data.frame of miRNA targets, with at least the following columns: 'family', 'rep.miRNA', 'feature', 'sites'. Alternatiely, the output of an aggregated scan of miRNA kdModels, with columns 'transcript', 'seed', 'score' (or 'log_kd'), 'n.8mer', etc.
miRNA.expression	A named vector of miRNAs expression values. miRNAs not in this vector are assumed to be not expressed in the system, and are not tested.
families	A named vector of miRNA families, with individual miRNAs as names. If not given, internal data from the package will be used (mouse miRNA families from targetScan).
cleanNames	Logical; whether to remove prefix from all miRNA names (default FALSE).
...	Passed to 'testEnrichment'

Value

an enrich.results object.

ETHZ-INS/enrichMiR documentation built on July 20, 2024, 12:03 a.m.