tcga_colon_blocks {epivizr} | R Documentation

## Example methylation data (blocks) for epivizr vignette.

### 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/

[Package epivizr version 2.20.0 Index]