Package 'mCSEAdata'

Title: Data package for mCSEA package
Description: Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality.
Authors: Jordi Martorell Marugán
Maintainer: Jordi Martorell Marugán <[email protected]>
License: GPL-2
Version: 1.32.0
Built: 2026-10-10 11:13:23 UTC
Source: https://github.com/bioc/mCSEAdata

Help Index

Data and examples for mCSEA package

Description

Association files between Illumina's 450K, EPIC and EPICv2 microarrays probes and promoters, CpG Islands and gene bodies. Annotation for the previous microarrays' probes. There are also sample data from EPIC platform and expression microarrays to test mCSEA functions and a necessary object for mCSEAPlot function.

Author(s)

Jordi Martorell Marugán Raúl López Domínguez

Maintainer: Jordi Martorell Marugán<[email protected]>

Examples

data(mcseadata)
data(bandTable)

Human chromosomes information

Description

bandTable contains chromosomes band information and centromer location from hg19 and hg38 genomes. It is used by mCSEAPlot() function to plot the chromosome track.

Usage

data(bandTable)

Format

matrix (bandTablehg19 and bandTablehg38), data.frame )

Source

Obtained with Gviz's IdeogramTrack() function.

Data and examples for mCSEA package

Description

Association files between Illumina's 450K and EPIC microarrays probes and promoters, CpG Islands and gene bodies. There are also sample data from EPIC platform to test mCSEA functions and annotation for 450K and EPIC probes.

Usage

data(mcseadata)

Format

matrix (betaTest and exprTest), data.frame (phenoTest), list (assocPromoters450k, assocPromotersEPIC, assocPromotersEPICv2, assocGenes450k, assocGenesEPIC, assocGenesEPICv2, assocCGI450k, assocCGIEPIC) and assocCGIEPICv2; and GRanges (annot450K, annotEPIC and annotEPICv2)

Source

betaTest and phenoTest are simulated data. exprTest was obtained from leukemiasEset package. annot450K, annotEPIC and annotEPICv2 were constructed with minfi package. assocPromoters450k, assocPromotersEPIC, assocPromotersEPICv2, assocGenes450k, assocGenesEPIC, assocGenesEPICv2, assocCGI450k, assocCGIEPIC and assocCGIEPICv2 were constructed from IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 and IlluminaHumanMethylationEPICv2anno.20a1.hg38 packages annotation data.