## ---- 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) ## -------------------------------------------------------------------------- metadata(bisc)$vcfHeader ## -------------------------------------------------------------------------- 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) ## -------------------------------------------------------------------------- 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 ## -------------------------------------------------------------------------- bisc.CpGindex <- CpGindex(bisc) show(bisc.CpGindex) bisc.CpGindex@hyperMethRegions