targetAnnotation: targetAnnotation

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

targetAnnotation

Description

Creates a new targetAnnotation object.

Usage

## S4 method for signature 'targetAnnotation'
show(object)

## S4 method for signature 'targetAnnotationDF'
show(object)

## S4 method for signature 'targetAnnotationDF'
head(x, n = 6L, ...)

## S4 method for signature 'targetAnnotationDF'
as.data.frame(x, name)

## S4 method for signature 'targetAnnotationMatrix'
as.data.frame(x, name)

## S4 method for signature 'targetAnnotationMatrix'
as.matrix(x, ...)

## S4 method for signature 'targetAnnotationDF'
as.matrix(x, ...)

## S4 method for signature 'targetAnnotationDF'
setTargetFeatures(x)

## S4 method for signature 'targetAnnotationMatrix'
setTargetFeatures(x)

## S4 method for signature 'targetAnnotationDF'
names(x)

## S4 method for signature 'targetAnnotationMatrix'
names(x)

## S4 method for signature 'targetAnnotationMatrix'
length(x)

## S4 method for signature 'targetAnnotationDF'
length(x)

## S4 method for signature 'targetAnnotationDF,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'targetAnnotationMatrix,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

targetAnnotation(
  x,
  content = "score",
  metadata = list(),
  set.properties = NULL,
  feature.synonyms = NULL,
  sets.synonyms = NULL
)

Arguments

x	A names list of items, or a (sparse) matrix with named dimensions, or a data.frame with at least the columns 'feature' and 'set', or a (h5/rds) file containing one of these.
content	The content of the matrix (e.g. 'score' or 'sites'); ignored if 'x' is a data.frame or list.
metadata	A list of metadata.
set.properties	A data.frame of additional set properties.
feature.synonyms	A named factor vector of feature synonyms.
sets.synonyms	A named factor vector of set names synonyms.

Value

An object of class 'targetAnnotation'; depending on 'x', either a 'targetAnnotationMatrix' or a 'targetAnnotationDF'.

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