tcga_colon_example: Example methylation data for epivizr vignette

In epiviz/epivizr-release: R Interface to epiviz web app

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)

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

Author(s)

Hector Corrada Bravo

Source

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

See Also

minfi-package

Examples

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

epiviz/epivizr-release documentation built on May 16, 2019, 8:18 a.m.