README

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## Source Codes of the CSMD1 Paper ##
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1. Figures
 This is where you would see the figure when you run the R codes explained below.

2. Rscript
 This is where the actual R codes are and the directory structure looks like this:

2.0. Library files 
 lib/local.R
 lib/multiplot.R
 lib/theme_publish.R
2.1. R scripts for the main figures (Fig1-Fig6)
 CSMD1.paper.figures.main.R
 CSMD1.Fig1.R
 CSMD1.Fig2.R
 CSMD1.Fig3.R
 CSMD1.Fig4.R
 CSMD1.Fig5.R
 CSMD1.Fig6.R
2.2. R scripts for the supplementary figures
 Suppl/CSMD1.Suppl.Fig3.CSMD1.DMR2.RoadMap.R
 Suppl/CSMD1.Suppl.Fig4.canonical.promoter.PT.R
 Suppl/CSMD1.Suppl.Fig6.putative.promoter.PT.R
 Suppl/CSMD1.Suppl.Fig8.putative.promoter.RoadMap.R
 Suppl/CSMD1.Suppl.Fig9.fetal.embryo.pheatmap.R

3. RData
 This is where the data/files are.
 However following files were omimitted due to the size limit (>25Mb)
	436M PT.CG.dt.meth.region.RData
	145M PT.CG.dt.merged.RData
	 88M hg19ensGene.sqlite
	 42M rnb.meth.diff.PT.RData

4. Track hub
 To browse methylation & expression level we presented in the paper,
 visit the links shown below:
 http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://www.obgyn.cam.ac.uk/TrackHub/CamObsGynaeHub.txt&org=human&db=hg19&position=chr8:2792000-3040000

 or,
 http://genome-euro.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://www.obgyn.cam.ac.uk/TrackHub/CamObsGynaeHub.txt&org=human&db=hg19&position=chr8:2792000-3040000

 Following two URLs are pre-configured track hubs links, which we presented in the supplemental figure 5 and 7: 
 Supplemental Figure S5. The reconstructed transcript of placenta CSMD1 compared with the reference gene annotation 
 https://goo.gl/yjflRX

 Supplemental Figure S7. Genome annotations that support the putative promoter region in the placenta
 https://goo.gl/i3xrNN

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Sungsam Gong <sung@bio.cc; ssg29@cam.ac.uk>
First created 8/Dec/2016
Last modified 9/Jan/2018