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\title{ELMER.data: Supporting data for the ELMER package}
\author {Lijing Yao [cre, aut], 
Ben Berman [aut], 
Peggy Farnham [aut]\\ 
Hui Shen [ctb], 
Peter Laird [ctb], 
Simon Coetzee [ctb]}

\begin{document}
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\maketitle

\tableofcontents
\section{Introduction}
This document provides an introduction of the \Rpackage{ELMER.data}, which contains 
supporting data for \Rpackage{ELMER}. \Rpackage{ELMER} is package using DNA methylation to 
identify enhancers, and correlates enhancer state with expression of nearby genes 
to identify one or more transcriptional targets. Transcription factor (TF) binding 
site analysis of enhancers is coupled with expression analysis of all TFs to 
infer upstream regulators. \Rpackage{ELMER} provide 5 necessary data for 
\Rpackage{ELMER} analysis:

1. Probes.motif: motif occurences within -/+100bp of probe sites on HM450K array.\\
2. human.TF: All human transcription factors.\\
3. Combined.TSS: Human TSS regions consist of TSS from hg19 UCSC gene and GENCODE V15.\\
4. motif.relavent.TFs: TFs may recognize the same motif.\\
5. Union.enhancer: A comprehensive list of genomic strong enhancers.\\

\subsection{Installing and loading ELMER.data}
To install this package, start R and enter
<<install, eval=FALSE>>=
source("http://bioconductor.org/biocLite.R")
biocLite("ELMER.data")
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<<loa, cache=TRUE>>=
library("ELMER.data")
library("GenomicRanges")
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\section{Contents}
\subsection{Probes.motif}

Probes.motif provide information for motif occurences within -/+100bp of probe 
sites on HM450K array. FIMO was used with a p-value < 0.0001 to scan a +/- 100bp 
region around each probe on HM450K using Factorbook motif position weight 
matrices (PWMs) and Jasper core human motif PWMs generated from the \Rpackage{MotifDb}.
This data set is used in get.enriched.motif function in \Rpackage{ELMER} to calculate 
Odds Ratio of motif enrichments for a given set of probes. This data is storaged 
in a matrix with 485512 row and 91 column. Each row is each probe regions and each 
column is motif from Factorbook and Jasper. The value 1 indicates the occurrence 
of a motif in a particular probe and 0 means no occurrence.

<<Probes.motif, cache=TRUE>>=
data("Probes.motif")
dim(Probes.motif)
str(Probes.motif)
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\subsection{human.TF}

human.TF list all human transcription factors information such as gene id, symbol.
It is a data frame contains symbols and gene ids for 1982 human trancription factor.
This data is used for get.TFs function in \Rpackage{ELMER} to identify the TFs whose 
expression highly associate with average DNA methylation motif sties.

<<human.TF, cache=TRUE>>=
data("human.TF")
dim(human.TF)
head(human.TF)
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\subsection{Combined.TSS}

Combined.TSS provide a comprehensive list of human hg19 annotated TSSs
from UCSC gene and GENCODE V15. This is used for identification of distal 
elements in get.feature.probe in \Rpackage{ELMER}. This data is stored as a GRanges
object containing coordinates of combined TSS.

<<Combined.TSS, cache=TRUE>>=
data("Combined.TSS")
Combined.TSS
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\subsection{motif.relavent.TFs}

motif.relavent.TFs list each motif and TFs that binding the motis. Multiple TFs may
recognize a same motif such as TF family.  This data is stored as a list whose elements 
are motifs and contents for each element are TFs which recognize the same motif that
is the name of the element. This data is used in function get.TFs in \Rpackage{ELMER} 
to identify the real regulator TF whose motif is enriched in a given set of probes 
and expression associate with average DNA methylation of these motif sites.

<<motif.relavent.TFs, cache=TRUE>>=
data("motif.relavent.TFs")
motif.relavent.TFs[1:2]
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\subsection{Union.enhancer}

Union.enhancer is a comprehensive list of genomic strong enhancers which comes 
from a combination of enhancers from the Roadmap Epigenomics Mapping Consortium (REMC) 
and the Encyclopedia of DNA Elements (ENCODE) Project, in which enhancers were 
identified using ChromHMM for 98 tissues or cell lines. We used the union of 
genomic elements labeled as EnhG1, EnhG2, EnhA1 or EnhA2 (representing intergenic 
and intragenic active enhancers) in any of the 98 cell types, resulting in a total 
of 389,967 non-overlapping enhancer regions. FANTOM5 enhancers (43,011) identified 
by eRNAs for 400 distinct cell types were added to this list. This data is stored 
as a GRanges object contains coordinates of this human comprehensive genomic enhancer set.
It will be used in get.feature.probe in \Rpackage{ELMER} to identify the distal enhancer
probes which are at least 2Kb awary from TSS regions and overlap with comprehensive 
enhancers.

<<Union.enhancer, cache=TRUE>>=
data("Union.enhancer")
Union.enhancer
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