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

testEnrichment

R Documentation

testEnrichment

Description

Creates an enrich.results object and performs enrichment analysis

Usage

testEnrichment(
  x,
  sets,
  background = NULL,
  tests = NULL,
  sets.properties = NULL,
  th.abs.logFC = 0,
  th.FDR = 0.05,
  minSize = 5,
  maxSize = Inf,
  gsea.maxSize = 3000,
  gsea.permutations = 4000,
  testOnlyAnnotated = FALSE,
  keepAnnotation = FALSE,
  field = NULL,
  BPPARAM = NULL,
  familyRound = NULL,
  checkSynonyms = TRUE,
  doCheck = TRUE,
  ...
)

Arguments

`x`	The signature in which to look for a signal. This can be either: 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'; A numeric vector of the signal with feature (e.g. genes) as names, in which case only tests based on a continuous signal will be possible; A logical vector of membership to the geneset of interest, with feature (e.g. genes) as names, in which case only tests based on a binary signal will be available. A vector of feature names; in this case the `background` argument will also be required, and only tests based on a binary signal will be available.
`sets`	Either a named list (or SimpleList) of features, or a data.frame (or DataFrame) with at least the columns 'set' and 'feature' (if the columns 'score' and 'sites' are also present, they will be used by the appropriate tests).
`background`	A character vector of background; ignored if 'x' is not a character vector.
`tests`	Character vector of the tests to perform. See `enrichMiR::availableTests` for the options.
`sets.properties`	Any further information about the sets; this can either be a data.frame (or DataFrame), with row.names corresponding to names of 'sets' (or to alternative names), or a named vector (e.g. miRNA expression values). If this is given, sets not included within this object will be discarded.
`th.abs.logFC`	The minimum absolute log2-foldchange threshold for a feature to be considered differentially-expressed (default 0). Ignored if 'x' is not a DEA data.frame.
`th.FDR`	The maximum FDR for a feature to be considered differentially- expressed (default 0.05). Ignored if 'x' is not a DEA data.frame.
`minSize`	The minimum size of a set to be tested (default 5).
`maxSize`	The maximum size of a set to be tested (default Inf).
`gsea.maxSize`	The maximum number of targets for a miRNA family to be tested using GSEA (default 300).
`gsea.permutations`	The number of permutations for GSEA (default 2000). See '?fgsea' for more information.
`testOnlyAnnotated`	Whether to excluded features that are no set from the background (default FALSE).
`field`	The field of 'x' to use as continuous signal. If omitted, defaults to 'sign(x$logFC)*-log10(x$FDR)'. Ignored if 'x' is not a data.frame.
`BPPARAM`	BiocParallel multithreading parameters. Used to multithread tests, and also within the 'gsea' test.
`doCheck`	Whether to check the inputs. This argument is for internal use and should not be disabled!