Package 'grndata'

Title: Synthetic Expression Data for Gene Regulatory Network Inference
Description: Simulated expression data for five large Gene Regulatory Networks from different simulators
Authors: Pau Bellot, Catharina Olsen, Patrick E Meyer
Maintainer: Pau Bellot <[email protected]>
License: GPL-3
Version: 1.45.0
Built: 2026-10-10 10:34:41 UTC
Source: https://github.com/bioc/grndata

Help Index

Available datasources

Description

Availabledata contains a character vector with the names of the datasources that the package contains.

Usage

data("Availabledata")

Format

A character vector with the names of the datasources.

Value

character vector with the names of the datasources.

Examples

data(Availabledata)
    cat(Availabledata)

Datasource and underlying network loading

Description

Function to load a gene expression datasource and the network that have generate it.

Usage

getData(datasource.name=NULL,getNet=TRUE)

Arguments

datasource.name

A character containing the name of network datasources to (default: NULL).
getNet

Logical specifying if the true underlying network should be returned (default: TRUE).

Details

If getNet is TRUE the function will return a list with two components:

  1. A data.frame with the specified datasoruce.

  2. A matrix with the true underlying network.

Value

The function getData loads the specified datasource by datasource.name and its true underlying network if it is specified by getNet.

Examples

# Get only datasource
    data <- getData(datasource.name="syntren300",getNet=FALSE)
    # Get the datasource and network in a list
    mydata <- getData(datasource.name="syntren1000")
    data <- mydata[[1]]
    net <- mydata[[2]]

Simulated Gene Expression Data

Description

Dataset containing 1565 samples and 1565 genes generated by the publicly available GNW generator using an ecoli source network with no added noise.

Usage

data(gnw1565.data)

Format

gnw1565.data is a data frame containing 1565 rows and 1565 columns. Each row contains a simulated microarray experiment and each column contains a gene. The dataset was generated with GNW generator which relies on ODEs for modeling gene regulation.

Value

data.frame containg the data.

Source

GNW v3.1 with source network : Ecoli

References

Schaffter, Thomas, Daniel Marbach, and Dario Floreano. "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods." Bioinformatics 27.16 (2011): 2263-2270.

See Also

gnw1565.net, gnw2000.data, rogers1000.data, syntren300.data, syntren1000.data

Examples

data(gnw1565.data)
    # Print size
    print(dim(gnw1565.data))

Simulated Gene Expression Data

Description

True underlying network used to generate the dataset at gnw1565.data.

Usage

data(gnw1565.net)

Format

true.net is the true underlying network used to generate the dataset loaded at gnw1565.data.

Value

matrix containg underlying network.

Source

GNW v3.1 with source network : Ecoli

References

Schaffter, Thomas, Daniel Marbach, and Dario Floreano. "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods." Bioinformatics 27.16 (2011): 2263-2270.

See Also

gnw1565.data, gnw2000.data, rogers1000.data, syntren300.data, syntren1000.data

Examples

data(gnw1565.net)
    # Number of directed edges
    nEdges<- sum(gnw1565.net)

Simulated Gene Expression Data

Description

Dataset containing 2000 samples and 2000 genes generated by the publicly available GNW generator using a yeast source network with no added noise.

Usage

data(gnw2000.data)

Format

gnw2000.data is a data frame containing 2000 rows and 2000 columns. Each row contains a simulated microarray experiment and each column contains a gene. The dataset was generated with GNW generator which relies on ODEs for modeling gene regulation.

Value

data.frame containg the data.

Source

GNW v3.1 with source network : Yeast

References

Schaffter, Thomas, Daniel Marbach, and Dario Floreano. "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods." Bioinformatics 27.16 (2011): 2263-2270.

See Also

gnw2000.net, gnw1565.data, rogers1000.data, syntren300.data, syntren1000.data

Examples

data(gnw2000.data)
    # Print size
    print(dim(gnw2000.data))

Simulated Gene Expression Data

Description

True underlying network used to generate the dataset at gnw2000.data.

Usage

data(gnw2000.net)

Format

true.net is the true underlying network used to generate the dataset loaded at gnw2000.data.

Value

matrix containg underlying network.

Source

GNW v3.1 with source network : Yeast

References

Schaffter, Thomas, Daniel Marbach, and Dario Floreano. "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods." Bioinformatics 27.16 (2011): 2263-2270.

See Also

gnw2000.data, gnw1565.data, rogers1000.data, syntren300.data, syntren1000.data

Examples

data(gnw2000.net)
    # Number of directed edges
    nEdges<- sum(gnw2000.net)

Simulated Gene Expression Data

Description

Dataset containing 1000 samples and 1000 genes generated by the publicly available generator using a power-law tail topology network with no added noise.

Usage

data(rogers1000.data)

Format

rogers1000.data is a data frame containing 1000 rows and 1000 columns. Each row contains a simulated microarray experiment and each column contains a gene.

Value

data.frame containg the data.

Source

sRogers with Power-law tail topology

References

Rogers, Simon, and Mark Girolami. "A Bayesian regression approach to the inference of regulatory networks from gene expression data." Bioinformatics 21.14 (2005): 3131-3137.

See Also

rogers1000.net, gnw1565.data, gnw2000.data, syntren300.data, syntren1000.data

Examples

data(rogers1000.data)
    # Print size
    print(dim(rogers1000.data))

Simulated Gene Expression Data

Description

True underlying network used to generate the dataset at rogers1000.data.

Usage

data(rogers1000.net)

Format

true.net is the true underlying network used to generate the dataset loaded at rogers1000.data.

Value

matrix containg underlying network.

Source

sRogers with Power-law tail topology

References

Rogers, Simon, and Mark Girolami. "A Bayesian regression approach to the inference of regulatory networks from gene expression data." Bioinformatics 21.14 (2005): 3131-3137.

See Also

rogers1000.data, gnw1565.data, gnw2000.data, syntren300.data, syntren1000.data

Examples

data(rogers1000.net)
    # Number of directed edges
    nEdges<- sum(rogers1000.net)

Simulated Gene Expression Data

Description

Dataset containing 1000 samples and 1000 genes generated by the publicly available SynTReN generator using an ecoli source network.

Usage

data(syntren1000.data)

Format

syntren1000.data is a data frame containing 1000 rows and 1000 columns. Each row contains a simulated microarray experiment and each column contains a gene.

Value

data.frame containg the data.

Source

SynTReN 1.1.3 with source network : ecoli\_nn.sif

References

Van den Bulcke, Tim, et al. "SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms." BMC Bioinformatics 7.1 (2006): 43.

See Also

gnw1565.data, gnw2000.data, rogers1000.data, syntren300.data

Examples

data(syntren1000.data)
    # Print size
    print(dim(syntren1000.data))

Simulated Gene Expression Data

Description

True underlying network used to generate the dataset at syntren1000.data.

Usage

data(syntren1000.net)

Format

syntren1000.net is the true underlying network used to generate the dataset loaded at syntren1000.data.

Value

matrix containg underlying network.

Source

SynTReN 1.1.3 with source network : ecoli\_nn.sif

References

Van den Bulcke, Tim, et al. "SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms." BMC Bioinformatics 7.1 (2006): 43.

See Also

syntren1000.data,gnw1565.data, gnw2000.data, rogers1000.data, syntren300.data

Examples

data(syntren1000.net)
    # Number of directed edges
    nEdges<- sum(syntren1000.net)

Simulated Gene Expression Data

Description

Dataset containing 800 samples and 300 genes generated by the publicly available SynTReN generator using an ecoli source network.

Usage

data(syntren300.data)

Format

syntren300.data is a data frame containing 800 rows and 300 columns. Each row contains a simulated microarray experiment and each column contains a gene.

Value

data.frame containg the data.

Source

SynTReN 1.1.3 with source network : ecoli\_nn.sif

References

Van den Bulcke, Tim, et al. "SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms." BMC Bioinformatics 7.1 (2006): 43.

See Also

syntren300.net, syntren1000.data, rogers1000.data, gnw1565.data, gnw2000.data

Examples

data(syntren300.data)
    # Print size
    print(dim(syntren300.data))

Simulated Gene Expression Data

Description

True underlying network used to generate the dataset at syntren300.data.

Usage

data(syntren300.net)

Format

true.net is the true underlying network used to generate the dataset loaded at syntren300.data.

Value

matrix containg underlying network.

Source

SynTReN 1.1.3 with source network : ecoli\_nn.sif

References

Van den Bulcke, Tim, et al. "SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms." BMC bioinformatics 7.1 (2006): 43.

See Also

syntren300.data, syntren1000.data, rogers1000.data, gnw1565.data, gnw2000.data

Examples

data(syntren300.net)
    # Number of directed edges
    nEdges<-sum(syntren300.net)

Simulated Toy example of Gene Expression Data

Description

Dataset containing 64 samples and 64 genes generated by the publicly available GNW generator using an ecoli source network.

Usage

data(toy.data)

Format

toy.data is a data frame containing 64 rows and 64 columns. Each row contains a simulated microarray experiment and each column contains a gene.

Value

data.frame containg the data.

Source

GNW v3.1 with source network : Example (Ecoli)

References

Schaffter, Thomas, Daniel Marbach, and Dario Floreano. "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods." Bioinformatics 27.16 (2011): 2263-2270.

See Also

toy.net

Examples

data(toy.data)
    # Print size
    print(dim(toy.data))

Simulated Toy example of Gene Expression Data

Description

True underlying network used to generate the dataset at toy.data.

Usage

data(toy.net)

Format

toy.net is the true underlying network used to generate the dataset loaded at toy.data.

Value

matrix containg underlying network.

Source

GNW v3.1 with source network : Example (Ecoli)

References

Schaffter, Thomas, Daniel Marbach, and Dario Floreano. "GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods." Bioinformatics 27.16 (2011): 2263-2270.

See Also

toy.data

Examples

data(toy.net)
    # Print size
    nEdges<- sum(toy.net)