## ----options,echo=FALSE----------------------------------------------- options(width=72) ## ----mpload,message=FALSE,cache=TRUE---------------------------------- library(methylPipe) library(BSgenome.Hsapiens.UCSC.hg18) ## ----methcall,message=FALSE,cache=TRUE-------------------------------- file_loc <- system.file('extdata', 'test_methcall', package='methylPipe') meth.call(files_location=file_loc, output_folder=tempdir(), no_overlap=TRUE, read.context="CpG", Nproc=1) ## ----bsprepare,message=FALSE,cache=TRUE------------------------------- file_loc <- system.file('extdata', 'H1_chr20_CG_10k.txt', package='methylPipe') #BSprepare(files_location=file_loc,output_folder=file_loc, tabix="/path-to-tabix/") uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184))) H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe') H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens) H1.db ## ----bsdataset,message=TRUE,cache=TRUE-------------------------------- IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe') IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens) H1.IMR90.set <- BSdataSet(org=Hsapiens, group=c("C","E"), IMR90=IMR90.db, H1=H1.db) H1.IMR90.set ## ----met1,fig.width=6,fig.height=5,out.width='.85\\textwidth',message=FALSE,cache=TRUE---- gr <- GRanges("chr20",IRanges(1,5e5)) sres <- mCsmoothing(H1.db, gr, Scorefun='sum', Nbins=50, plot=TRUE) ## ----desstats,fig.width=6,fig.height=5,out.width='.85\\textwidth',message=FALSE, fig.keep="all",fig.show="asis",cache=TRUE---- stats.set <- BSdataSet(org=Hsapiens, group=c("C","C","E","E"), IMR_1=IMR90.db, IMR_2=IMR90.db, H1_1=H1.db,H1_2=H1.db) stats_res <- methstats(stats.set,chrom="chr20",mcClass='mCG', Nproc=1) stats_res ## ----met2,message=FALSE,cache=TRUE------------------------------------ gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe') load(gr_file) resmC <- mapBSdata2GRanges(GenoRanges=GR_chr20, Sample=H1.db, context='CG') head(resmC[[4]]) ## ----met3,message=FALSE,cache=TRUE------------------------------------ gec.H1 <- profileDNAmetBin(GenoRanges=GR_chr20, Sample=H1.db, mcCLASS='mCG', nbins=3) binmC(gec.H1)[4:5,] binC(gec.H1)[4:5,] binrC(gec.H1)[4:5,] ## ----subset,message=FALSE,cache=TRUE---------------------------------- gec1 <- gec.H1[start(gec.H1) < 153924] gec2 <- gec.H1[start(gec.H1) > 153924] ## ----gecset,message=FALSE,cache=TRUE---------------------------------- gecIMR_file <- system.file('extdata', 'gec.IMR90.Rdata', package='methylPipe') load(gecIMR_file) gel <- GElist(gecIMR90=gec.IMR90, gecH1=gec.H1) print(names(gel)) ## ----pmeth,fig.width=5,fig.height=5,out.width='.85\\textwidth',message=FALSE,cache=TRUE---- library(TxDb.Hsapiens.UCSC.hg18.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg18.knownGene gel <- GElist(gecIMR90=gec.IMR90[1:10], gecH1=gec.H1[1:10]) plotMeth(gel, colors=c("red","blue"), datatype=c("mC","mC"), yLim=c(.025, .025), brmeth=list(IMR90=IMR90.db, H1=H1.db), mcContext="CG", transcriptDB=txdb, chr="chr20", start=14350, end=277370, org=Hsapiens) ## ----dmr1,message=FALSE,cache=TRUE------------------------------------ DMRs <- findDMR(object= H1.IMR90.set, Nproc=1, ROI=GR_chr20, MCClass='mCG', dmrSize=6, dmrBp=800) head(DMRs) ## ----dmr2,message=FALSE,cache=TRUE------------------------------------ hyper.DMRs.conso <- consolidateDMRs(DmrGR=DMRs, pvThr=0.05, GAP=100, type="hyper") hyper.DMRs.conso[1:4] ## ----info,echo=TRUE--------------------------------------------------- sessionInfo()