exampleDesign {CAGEfightR} | R Documentation

## Example CAGE Data

### Description

Subset of the CAGE dataset from the paper 'Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo'. CTSS data from subsets of chr18 and chr19 across 3 mouse (mm9 ) samples are included. Datasets can be loaded with the data function.

### Usage

    exampleDesign

    exampleCTSSs

    exampleUnidirectional

    exampleBidirectional

    exampleGenes

### Format

Example data from various stages of CAGEfightR:

exampleDesign

  DataFrame: Description of samples, including .bw filenames

exampleCTSS

  RangedSummarizedExperiment: CTSSs

exampleUnidirectional

  RangedSummarizedExperiment: Unidirectional or Tag Clusters

exampleBidirectionalCluster

  RangedSummarizedExperiment: Bidirectional clusters

exampleGenes

  RangedSummarizedExperiment: Genes

An object of class `RangedSummarizedExperiment` with 41256 rows and 3 columns.

An object of class `RangedSummarizedExperiment` with 21008 rows and 3 columns.

An object of class `RangedSummarizedExperiment` with 377 rows and 3 columns.

An object of class `RangedSummarizedExperiment` with 127 rows and 3 columns.

### Source

http://pubs.acs.org/doi/abs/10.1021/acsnano.6b07533

### Examples

    data(exampleDesign)
    data(exampleCTSSs)
    data(exampleUnidirectional)
    data(exampleBidirectional)
    data(exampleGenes)

[Package CAGEfightR version 1.10.0 Index]