EzDataset-class: The R5 class representing a dataset
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

EzDataset-class

R Documentation

The R5 class representing a dataset

Description

Use this to create an object of the class EzDataset that contains the necessary fields for the input and output datasets.

Fields

file: a character representing the file path of the dataset's contents.
meta: a data.frame containing the information about the samples.
colNames: a character vector of the column names in meta.
tags: a list with possible tags for colNames.
isModified: whether the dataset has been modified.

Methods

columnHasTag(tag): Checks each column whether its tags matches tag.
getColumn(names): Gets the column(s) selected with names.
getFullPaths(name): Gets the files in the nameed column prepended with the dataRoot.
getLength(): Gets the number of samples.
getNames(): Gets the row names.
setColumn(name, values): Sets the column selected with name to values. If values is NULL the column gets removed
subset(samples): Subsets the meta field keeping samples and generates a new EzDataset

Functions

ezTagListFromNames(names): Gets the tags from names that are in the format [tag].

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

file = system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE)
dataRoot = system.file(package="ezRun", mustWork = TRUE)
ds = EzDataset$new(file=file, dataRoot=dataRoot)
ds$file
ds$meta
ds$getColumn("Read1")
ds$getFullPaths("Read1")
ds2 = ds$copy()
ds2$setColumn("Read1","replacement")
ds$columnHasTag("File")
ds$getNames()
ds$meta$"Genotype [Factor]"[1] = "a"
ds2 = EzDataset$new(meta = ds$meta, dataRoot=dataRoot)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.