exampleDesign: Example CAGE Data

In CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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)

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.