tcga_colon_expression


A <code><a rd-options="SummarizedExperiment" href="/link/RangedSummarizedExperiment?package=epivizr&version=2.2.3&to=SummarizedExperiment" data-mini-rdoc="SummarizedExperiment::RangedSummarizedExperiment">RangedSummarizedExperiment</a></code> object containing exon-level
counts from RNAseq data for colon tumor and normal tissue from the TCGA project. 
Only exons in human chromosome 11 are included.


datasets

This package provides connections to the
epiviz web app (http://epiviz.cbcb.umd.edu) for interactive
visualization of genomic data. Objects in R/bioc interactive
sessions can be displayed in genome browser tracks or plots to
be explored by navigation through genomic regions. Fundamental
Bioconductor data structures are supported (e.g., GenomicRanges
and RangedSummarizedExperiment objects), while providing an easy
mechanism to support other data structures (through package epivizrData).
Visualizations (using d3.js) can be easily added to the web app as well.

Hector Bravo

epivizr

R Interface to epiviz web app

tcga_colon_expression function

A <code><a rd-options="SummarizedExperiment" href="/link/RangedSummarizedExperiment?package=epivizr&version=2.2.3&to=SummarizedExperiment" data-mini-rdoc="SummarizedExperiment::RangedSummarizedExperiment">RangedSummarizedExperiment</a></code> object with 12,800 rows (exons) and 40 samples.
 <dl>
   <dt><code>assay(tcga_colon_expression)</code></dt><dd>exon-level count matrix</dd> <dt><code>colData(tcga_colon_expression)</code></dt><dd>a <code>DataFrame</code> containing sample information. 
     Normal/Tumor status is given in column <code>sample_type</code></dd> </dl>

Format

TCGA project: <a href="https://tcga-data.nci.nih.gov/tcga/">https://tcga-data.nci.nih.gov/tcga/</a>

Source

A <code><a href="RangedSummarizedExperiment" rd-options="SummarizedExperiment">RangedSummarizedExperiment</a></code> object containing exon-level
counts from RNAseq data for colon tumor and normal tissue from the TCGA project. 
Only exons in human chromosome 11 are included.

tcga_colon_expression: Example exon-level RNAseq data from TCGA project for epivizr vignette.

Description

Usage

Arguments

Value

Format

Source