tcga_colon_example: Example methylation data for epivizr vignette

Description

This package contains example results from methylation analysis of human chromosome 11 using the minfi-package package of TCGA 450k beadarray samples.

Usage

data(tcga_colon_example)

Arguments

Format

Two GRanges objects. The first colon_blocks, described large regions of methylation difference between tumor and normal samples. It has the following as metadata:

value: average smooth methylation difference within block
area: block area estimate (abs(value) * length)
cluster: id of cluster blockgroup within which block occurs
indexStart: index of first cluster in block
indexEnd: index of last cluster in block
L: number of clusters in block
clusterL: number of probes in block
p.value: permutation p.value based on difference conditioned on length
fwer: family-wise error rate estimate based on difference conditioned on length
p.valueArea: permutation p.value based on area
fwerArea: family-wise error rate estimate based on area

The second, colon_curves, is probe cluster-level methylation estimates. It has the following as element metadata:

id: probe cluster id
type: probe cluster type
blockgroup: probe cluster block group
diff: raw methylation percentage difference between normal and tumor
smooth: smooth methylation percentage difference between normal and tumor
normalMean: mean methylation estimate for normal samples
cancerMean: mean methylation estimate for cancer samples

Source

TCGA project: https://tcga-data.nci.nih.gov/tcga/

Examples

Run this code

data(tcga_colon_example)
show(colon_blocks)
show(colon_curves)