tcga_colon_blocks: Example methylation data (blocks) for epivizr vignette.

In epiviz/epivizr: R Interface to epiviz web app

Description

Example results from methylation analysis of human chromosome 11 using the minfi::minfi-package package of TCGA 450k beadarray samples. This object contains large regions of methylation difference between tumor and normal samples obtained from minfi::blockFinder().

Usage

data(tcga_colon_blocks)

Format

A GRanges object with 129 and mcols:

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

Source

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

epiviz/epivizr documentation built on Aug. 5, 2021, 6:37 p.m.