## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("biscuiteer") ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("trichelab/biscuiteerData") # BiocManager::install("trichelab/biscuiteer") ## ----------------------------------------------------------------------------- library(biscuiteer) orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz", package="biscuiteer") orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz", package="biscuiteer") bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf, merged = FALSE) ## ----------------------------------------------------------------------------- biscuitMetadata(bisc) ## ----------------------------------------------------------------------------- shuf_bed <- system.file("extdata", "MCF7_Cunha_chr11p15_shuffled.bed.gz", package="biscuiteer") shuf_vcf <- system.file("extdata", "MCF7_Cunha_shuffled_header_only.vcf.gz", package="biscuiteer") bisc2 <- readBiscuit(BEDfile = shuf_bed, VCFfile = shuf_vcf, merged = FALSE) comb <- unionize(bisc, bisc2) ## ----------------------------------------------------------------------------- epibed.nome <- system.file("extdata", "hct116.nome.epibed.gz", package="biscuiteer") epibed.bsseq <- system.file("extdata", "hct116.bsseq.epibed.gz", package="biscuiteer") epibed.nome.gr <- readEpibed(epibed = epibed.nome, genome = "hg19", chr = "chr1") epibed.bsseq.gr <- readEpibed(epibed = epibed.bsseq, genome = "hg19", chr = "chr1") ## ----------------------------------------------------------------------------- reg <- GRanges(seqnames = rep("chr11",5), strand = rep("*",5), ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7), end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7)) ) frac <- getLogitFracMeth(bisc, minSamp = 1, r = reg) frac ## ----------------------------------------------------------------------------- ages <- WGBSage(comb, "horvath") ages