软件链接地址：https://code.google.com/p/edmr/
该软件是可以基于对methylkit 软件包进行 进一步处理的，在处理和找寻差异甲基化为点和区域，分析的要比 methylkit更加细致。建议使用methylkit主要是对样本间甲基化水平的各种评估，但是寻找差异还是建议使用edmr软件包。
使用的相关脚本如下：
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | ############################################# library(edmr) library(methylKit) library(GenomicRanges) library(mix tools) #首先使用bismark，然后使用methylkit(具体可参见：https://www.plob.org/2014/10/22/8831.html) file.list=list( "1h_CpG.txt","HL_CpG.txt") myobj=read(file.list,sample.id=list("h0","L0"),assembly="hg19",treatment=c(0,1)) meth=unite(myobj, destrand=FALSE) myDiff=calculateDiffMeth(meth,num.cores=8) # fitting the bimodal normal distribution to CpGs distribution tiff("h0_VS_L0.tiff") myMixmdl=myDiff.to.mixmdl(myDiff, plot=T, main="h0_VS_L0") dev.off() # plot cost function and the determined distance cutoff tiff("h0_VS_L0_cost_function.tiff") plotCost(myMixmdl, main="cost function") dev.off() # calculate all DMRs candidate mydmr=edmr(myDiff, mode=1, ACF=TRUE) # further filtering the DMRs mysigdmr=filter.dmr(mydmr) ## annotation加载注释文件这两个文件可以在edmr上下载 # get genebody annotation GRangesList object genebody=genebody.anno(file="/DG/home/fyc/methylation/eDMR/hg19_refseq_all_types.bed") # get CpG islands and shores annotation cpgi=cpgi.anno(file="/DG/home/fyc/methylation/eDMR/hg19_cpgisland_all.bed") # plot the eDMR genebody annotation tiff("eDMR_genebody_annotation") plot.dmr.distr(mysigdmr, genebody, main="eDMR genebody annotation", xlab="DMR count") dev.off() # plot the eDMR CpG islands and shores annotation tiff("eDMR_CpG_annotation") plot.dmr.distr(mysigdmr, cpgi, main="eDMR CpG islands and shores annotation", xlab="DMR count") dev.off() # prepare genes for pathway analysis with significant DMRs at its promoter regions dmr.genes=get.dmr.genes(myDMR=mysigdmr, subject=genebody$promoter, id.type="gene.symbol") dmr.genes ########### |
原文来自：http://blog.sina.com.cn/s/blog_83f77c940102v7js.html
