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

In HCBravoLab/epivizrChart: R interface to epiviz web components

Description

Example results from methylation analysis of human chromosome 11 using the minfi 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 GenomicRanges::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/

HCBravoLab/epivizrChart documentation built on Aug. 10, 2021, 1:05 p.m.