## ----dependencies, warning=FALSE, message=FALSE------------------------------- library(bsseq) ## ----BSchr22------------------------------------------------------------------ data(BS.chr22) BS.chr22 ## ----ov-granges--------------------------------------------------------------- head(granges(BS.chr22), n = 4) ## ----ov-getCoverage----------------------------------------------------------- head(getCoverage(BS.chr22, type = "M"), n = 4) head(getCoverage(BS.chr22), n = 4) ## ----using-examples----------------------------------------------------------- head(start(BS.chr22), n = 4) head(seqnames(BS.chr22), n = 4) sampleNames(BS.chr22) pData(BS.chr22) dim(BS.chr22) BS.chr22[1:6,1] subsetByOverlaps(BS.chr22, GRanges(seqnames = "chr22", ranges = IRanges(start = 1, end = 2*10^7))) ## ----data-bsseq--------------------------------------------------------------- M <- matrix(0:8, 3, 3) Cov <- matrix(1:9, 3, 3) BStmp <- BSseq(chr = c("chr1", "chrX", "chr1"), pos = 1:3, M = M, Cov = Cov, sampleNames = c("A1","A2", "B")) ## ----data-order--------------------------------------------------------------- granges(BStmp) BStmp <- orderBSseq(BStmp, seqOrder = c("chr1", "chrX")) granges(BStmp) ## ----data-chrSelect----------------------------------------------------------- chrSelectBSseq(BStmp, seqnames = "chr1", order = TRUE) ## ----data-combine------------------------------------------------------------- BStmp2 <- combine(BStmp, BS.chr22[1:3,]) granges(BStmp2) getCoverage(BStmp2) ## ----data-collapse------------------------------------------------------------ collapseBSseq(BStmp, group = c("A", "A", "B")) ## ----getCoverage1------------------------------------------------------------- head(getCoverage(BS.chr22, type = "Cov"), n = 4) head(getCoverage(BS.chr22, type = "M"), n = 4) ## ----regions------------------------------------------------------------------ regions <- GRanges(seqnames = c("chr22", "chr22"), ranges = IRanges(start = 1.5 * 10^7 + c(0,200000), width = 1000)) getCoverage(BS.chr22, regions = regions, what = "perRegionTotal") ## ----getCoverage2------------------------------------------------------------- getCoverage(BS.chr22, regions = regions, what = "perBase") ## ----getMeth------------------------------------------------------------------ getMeth(BS.chr22, regions, type = "raw") getMeth(BS.chr22, regions[2], type = "raw", what = "perBase") ## ----locateScript, results="hide"--------------------------------------------- system.file("scripts", "get_BS.chr22.R", package = "bsseq") ## ----BSmooth------------------------------------------------------------------ BS.chr22.1 <- BSmooth(BS.chr22[,"r1"], verbose = TRUE) BS.chr22.1 ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()