tcga_colon_curves


Example results from methylation analysis of human chromosome 11 using the <code><a rd-options="minfi" href="/link/minfi-package?package=epivizr&version=2.2.3&to=minfi" data-mini-rdoc="minfi::minfi-package">minfi-package</a></code> package 
of TCGA 450k beadarray samples. This object contains probe cluster level methylation estimates from 
<code><a rd-options="minfi" href="/link/blockFinder?package=epivizr&version=2.2.3&to=minfi" data-mini-rdoc="minfi::blockFinder">blockFinder</a></code>.


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_curves function

A <code><a rd-options="GenomicRanges" href="/link/GRanges?package=epivizr&version=2.2.3&to=GenomicRanges" data-mini-rdoc="GenomicRanges::GRanges">GRanges</a></code> object with 7135 ranges and <code>mcols</code>: <dl>
 <dt><code>id</code></dt><dd>probe cluster id</dd> <dt><code>type</code></dt><dd>probe cluster type</dd> <dt><code>blockgroup</code></dt><dd>probe cluster block group</dd> <dt><code>diff</code></dt><dd>raw methylation percentage difference between normal and tumor</dd> <dt><code>smooth</code></dt><dd>smooth methylation percentage difference between normal and tumor</dd> <dt><code>normalMean</code></dt><dd>mean methylation estimate for normal samples</dd> <dt><code>cancerMean</code></dt><dd>mean methylation estimate for cancer samples</dd> </dl>

Format

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

Source

Example results from methylation analysis of human chromosome 11 using the <code><a href="minfi-package" rd-options="minfi">minfi-package</a></code> package 
of TCGA 450k beadarray samples. This object contains probe cluster level methylation estimates from 
<code><a href="blockFinder" rd-options="minfi">blockFinder</a></code>.

tcga_colon_curves: Example methylation data (smoothed methylation levels) for epivizr vignette

Description

Usage

Arguments

Value

Format

Source