Package: ChAMPdata 2.44.0

Yuan Tian

ChAMPdata: Data Packages for ChAMP package

Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.

Authors:Yuan Tian [ctb,aut], Tiffany Morris [cre,aut], Lee Stirling [ctb] and Andrew Teschendorff [ctb]

# Install 'ChAMPdata' in R:

install.packages('ChAMPdata', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

bloodCtl - Blood Control data
CellTypeMeans27K - Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.
CellTypeMeans450K - Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.
EPIC.manifest.hg19 - SNP annotation for EPIC array.
EPIC.manifest.pop.hg19 - SNP annotation for EPIC array for different population.
hm450.manifest.hg19 - SNP annotation for 450K array.
hm450.manifest.pop.hg19 - SNP annotation for 450K array for different population. Data is based on hg19.
illumina450Gr - GRange Struct of illumina 450K array.
MatchGeneName - MatchGeneName
multi.hit - Multi.hit information.
PathwayList - PathwayList, used in champ.GSEA
probe.features - Probe.features
probeInfoALL.lv - Probe Info Data for use with the BMIQ normalization.
snp.hit - CpG site related to SNP sites information.

On BioConductor:ChAMPdata-2.45.1(data/experiment 3.24)ChAMPdata-2.44.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:d6bcdab384 (on RELEASE_3_23). Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	178
linux-devel	WARNING	495
source / vignettes	OK	2134
linux-release	WARNING	476

Exports:

Help page	Topics
Data Packages to use with the ChAMP Chip Analysis Methylation Pipeline	ChAMPdata-package ChAMPdata
Anno450K	Anno450K
AnnoEPIC	AnnoEPIC
Blood Control data	bloodCtl
Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.	CellTypeMeans27K
Cell-type purified whole blood methylation CpG Sites for use with the RefBaseEWAS cell-type correction function.	CellTypeMeans450K
ControlProbes450K	ControlProbes450K
ControlProbesEPIC	ControlProbesEPIC
SNP annotation for EPIC array.	EPIC.manifest.hg19
SNP annotation for EPIC array for different population.	EPIC.manifest.pop.hg19
Simulation EPIC beadarray Dataset.	EPICSimData
SNP annotation for 450K array.	hm450.manifest.hg19
SNP annotation for 450K array for different population. Data is based on hg19.	hm450.manifest.pop.hg19
hprdAsigH PPI network dataset for champ.FEM function.	hprdAsigH
GRange Struct of illumina 450K array.	illumina450Gr
GRange S4 Object of illumina EPIC array.	illuminaEPICGr
MatchGeneName	MatchGeneName
multi.hit information.	multi.hit
PathwayList, used in champ.GSEA()	PathwayList
probe.features	probe.features
probe.features.epic	probe.features.epic
Probe Info Data for use with the BMIQ normalization.	probeInfoALL.epic.lv
Probe Info Data for use with the BMIQ normalization.	probeInfoALL.lv
CpG site related to SNP sites information.	snp.hit
Test dataset.	testDataSet