README for Supplementary Code (Lesch et al., 2016)

R scripts in this supplement should be run from within the same directory as the Supplementary Data files listed below. No additional input is required.


Data files included in the Supplementary Data directory:

1) Processed H3K4me3, H3K27me3, and expression (FPKM) values for pachytene spermatocytes and round spermatids from each biological sample.  

	human 1		SuppData1_hs1.txt
	human 2		SuppData2_hs2.txt
	human 3		SuppData3_hs3.txt
	rhesus 1	SuppData4_rh1.txt
	rhesus 2	SuppData5_rh2.txt
	mouse 1		SuppData6_mm1.txt
	mouse 2		SuppData7_mm2.txt
	bull 		SuppData8_bt1.txt
	opossum 1	SuppData9_md1.txt
	opossum 2	SuppData10_md2.txt
	chicken		SuppData11_gg1.txt
	
2) Sets of orthologous genes in the five mammalian species and in the five mammalian 
species plus chicken.

	five mammals	SuppData12_fiveway_orthologs.txt
	six amniotes	SuppData13_sixway_orthologs.txt
	


R scripts included in the Supplementary Code directory:

	heatmaps.R		
	Plot heatmaps of gene expression vs. H3K4me3 and H3K27me3 signal (Fig. 1b and Supplementary Fig. 2a)

	divergencePlots.R	
	Calculate dissimilarity matrices for processed ChIP and RNA-seq datasets, plot clustering dendrograms, and plot dissimilarity against divergence time. (Fig. 1c, 1d)

	pairwiseOverlaps.R	
	Find overlapping bivalent genes between pairs of species. (Fig. 2e)

	findIntersections.R	
	Get all (exclusive) intersections of poised gene sets for five mammals and save a list of each intersecting set.  

	varyThresholds.R	
	Plot number of five-way poised genes called as H3K4me3, H3K27me3, and expression thresholds vary. (Supplementary Fig. 5a)