ezDesignFromDataset: Gets the design from the dataset

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Gets the design from the dataset

Description

Gets the design from the dataset or parameters, if specified.

Usage

ezDesignFromDataset(dataset, param = NULL)

ezConditionsFromDesign(design, maxFactors = 2)

ezConditionsFromDataset(dataset, param = NULL, maxFactors = 2)

addReplicate(x, sep = "_", repLabels = 1:length(x))

Arguments

dataset	a data.frame from the meta field of an EzDataset.
param	a list of parameters to specify the factors directly using param$factors.

Value

Returns the factorial design of the dataset.

Functions

• ezConditionsFromDesign: Gets the conditions from the design. Use maxFactors to limit the amount of factors.

• ezConditionsFromDataset: A wrapper to get the conditions directly from the dataset.

• addReplicate: add a replicate id to make values unique

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

file = system.file("extdata/yeast_10k/dataset.tsv", package="ezRun", mustWork = TRUE)
ds = EzDataset$new(file=file, dataRoot=NULL)
design = ezDesignFromDataset(ds$meta)
cond = ezConditionsFromDesign(design)
addReplicate(apply(design, 1, paste, collapse="_"))
addReplicate(cond)

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.