| Title: | Data Package for DMRcate |
|---|---|
| Description: | This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate. |
| Authors: | Tim Peters |
| Maintainer: | Tim Peters <[email protected]> |
| License: | GPL-3 |
| Version: | 2.30.0 |
| Built: | 2026-10-10 11:11:02 UTC |
| Source: | https://github.com/bioc/DMRcatedata |
SNP annotation, cross-hybridising probes, XY probes, and gene annotation for hg19, hg38 and mm10
Tim Peters, Immunogenomics Laboratory, Garvan Institute of Medical Research
Maintainer: Tim Peters<[email protected]>
data(crosshyb) data(snpsall) data(hg19.grt) data(hg19.generanges)data(crosshyb) data(snpsall) data(hg19.grt) data(hg19.generanges)
Matrix of EPICv2 beta values from Noguera-Castells et al. (2023) consisting of five B cell acute lymphoblastic leukaemia (BALL) and five T cell acute lymphoblastic leukaemia (TALL) samples for DMR calling.
data(ALLbetas)data(ALLbetas)
data.frame
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE222nnn/GSE222919/suppl/GSE222919_processed_data.txt.gz
This is a character vector of Illumina probes whose probe sequence promiscuously aligns to non-target sections of the genome with a matching of 47bp or higher.
data(crosshyb)data(crosshyb)
character
https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM2_ESM.csv (accessed September 2019) https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM3_ESM.csv (accessed September 2019) http://www.sickkids.ca/MS-Office-Files/Research/Weksberg Lab/48639-non-specific-probes-Illumina450k.xlsx (accessed September 2019)
This is a data.frame of Illumina probes from EPICv2 whose target CpG lies on or near a known SNP. SNP ID, distance and minor allele frequency are all reported here.
data(snpsall)data(snpsall)
data.frame
This data set gives the genomic intervals of all gene regions in the Ensembl Release 75 of hg19.
data(hg19.generanges)data(hg19.generanges)
A GRanges object with 57773 intervals.
ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
This is a GeneRegionTrack formulated from TxDb.Hsapiens.UCSC.hg19.knownGene.
data(hg19.grt)data(hg19.grt)
GeneRegionTrack
This data set gives the genomic intervals of all gene regions in the Ensembl Release 102 of hg38.
data(hg38.generanges)data(hg38.generanges)
A GRanges object with 60616 intervals.
ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/Homo_sapiens.GRCh38.102.chr.gtf.gz
This is a GeneRegionTrack formulated from TxDb.Hsapiens.UCSC.hg38.knownGene.
data(hg38.grt)data(hg38.grt)
GeneRegionTrack
This data set gives the genomic intervals of all gene regions in the Ensembl Release 102 of mm10.
data(mm10.generanges)data(mm10.generanges)
A GRanges object with 55401 intervals.
ftp://ftp.ensembl.org/pub/release-96/gtf/mus_musculus/Mus_musculus.GRCm38.102.chr.gtf.gz
This is a GeneRegionTrack formulated from TxDb.Mmusculus.UCSC.mm10.knownGene.
data(mm10.grt)data(mm10.grt)
GeneRegionTrack
This is a data.frame of Illumina probes from EPICv1 and 450K whose target CpG lies on or near a known SNP. SNP ID, distance and minor allele frequency are all reported here.
data(snpsall)data(snpsall)
data.frame
https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM4_ESM.csv (accessed September 2019) https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM5_ESM.csv (accessed September 2019) https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM6_ESM.csv (accessed September 2019) http://www.sickkids.ca/MS-Office-Files/Research/Weksberg Lab/48640-polymorphic-CpGs-Illumina450k.xlsx (accessed September 2019)
This is a character vector of Illumina probes whose target CpG site is on a sex chromosome.
data(XY.probes)data(XY.probes)
character