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\title{The \texttt{DMRcatedata} package user's guide}

\author{Peters TJ, Buckley MJ, Statham AL, Pidsley R, Zotenko E, Clark SJ, Molloy PL}
\maketitle

\section*{Package Contents}

\texttt{DMRcatedata} accompanies the \texttt{DMRcate} package, providing data for examples, probe filtering and transcript annotation.

<<libr, message=FALSE, warning=FALSE>>=
library(DMRcatedata)
data(crosshyb)

#Proximal SNPs to EPICv1 and 450K
data(snpsall)

#Proximal SNPs to EPICv2
data(epicv2snps)

data(hg19.grt)
data(hg19.generanges)

#Betas for EPICv2 
data(ALLbetas)
@

Ten objects are contained in \texttt{DMRcatedata}. 
\texttt{crosshyb} is a factor listing EPICv1 and 450K probe IDs potentially confounded by cross-hybridisation to other parts of the genome\cite{Pidsley}\cite{Chen}. It is used internally by \texttt{rmSNPandCH()}.


\texttt{snpsall} is a data.frame containing probes from 450K and EPICv1 that are potentially confounded by a SNP or indel variant\cite{Pidsley}. It lists the ID, distance (in nucleotides) to the CpG in question, and minor allele frequency for each associated variant. \texttt{epicv2snps} contains the same but for the EPICv2 array.


\texttt{XY.probes} is a vector of EPICv1 and 450K Illumina probes whose targets are on human sex chromosomes.


Objects named \texttt{.*\.(grt|generanges)} are annotation objects that are needed by \texttt{extractRanges()} and \texttt{DMR.plot()} respectively. hg38 and mm10 objects have been parsed from Release 96 of Ensembl, and hg19 from Release 75. These are accessed within the environment of the aforementioned functions.

\texttt{ALLbetas} is a matrix of EPICv2 beta values from Noguera-Castells et al. (2023)\cite{Noguera} consisting of five B cell acute lymphoblastic leukaemia (BALL) and five T cell acute lymphoblastic leukaemia (TALL) samples for DMR calling.

\section*{Sources}
\begin{itemize}
  \item \texttt{snpsall} sourced from \url{https://static-content.springer.com/esm/art\%3A10.1186\%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM4_ESM.csv}, \url{https://static-content.springer.com/esm/art\%3A10.1186\%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM5_ESM.csv}, \url{https://static-content.springer.com/esm/art\%3A10.1186\%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM6_ESM.csv}, \url{http://www.sickkids.ca/MS-Office-Files/Research/Weksberg Lab/48640-polymorphic-CpGs-Illumina450k.xlsx} (accessed October 2016) 
  \item \texttt{crosshyb} sourced from \url{https://static-content.springer.com/esm/art\%3A10.1186\%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM2_ESM.csv}, \url{https://static-content.springer.com/esm/art\%3A10.1186\%2Fs13059-016-1066-1/MediaObjects/13059_2016_1066_MOESM3_ESM.csv} (accessed October 2016) and \url{http://www.sickkids.ca/MS-Office-Files/Research/Weksberg Lab/48639-non-specific-probes-Illumina450k.xlsx}, (accessed February 2014). 
  \item {ALLbetas} sourced from \url{https://ftp.ncbi.nlm.nih.gov/geo/series/GSE222nnn/GSE222919/suppl/GSE222919_processed_data.txt.gz}, (accessed February 2024).
  \item {epicv2snps} sourced from \url{https://static-content.springer.com/esm/art\%3A10.1186\%2Fs12864-024-10027-5/MediaObjects/12864_2024_10027_MOESM4_ESM.csv} (Accessed March 2024). 
\end{itemize}

\begin{thebibliography}{9}

\bibitem{Pidsley}
  Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, 
  Van Dijk S, Muhlhausler B, Stirzaker C, Clark SJ. Critical evaluation of 
  the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA 
  methylation profiling. \emph{Genome Biology}. 2016 17(1), 208.

\bibitem{Chen}
  Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R. 
  Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. 
  \emph{Epigenetics}. 2013 Jan 11;8(2).

\bibitem{Noguera}
  Noguera-Castells A, Garcia-Prieto CA, Alvarez-Errico D, Esteller M. Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome. \emph{Epigenetics} 2023 Dec;18(1):2185742.
  
\end{thebibliography}

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