## ----setup, eval=TRUE, include=FALSE------------------------------------------ library(epivizrChart) library(Homo.sapiens) ## ----------------------------------------------------------------------------- data(tcga_colon_blocks) ## ----------------------------------------------------------------------------- epiviz_env <- epivizEnv(chr="chr11", start=118000000, end=121000000) genes_track <- epiviz_env$plot(Homo.sapiens) blocks_track <- epiviz_env$plot(tcga_colon_blocks, datasource_name="450kMeth") ## ----------------------------------------------------------------------------- file1 <- Rsamtools::BamFile("http://1000genomes.s3.amazonaws.com/phase3/data/HG01879/alignment/HG01879.mapped.ILLUMINA.bwa.ACB.low_coverage.20120522.bam") file2 <- rtracklayer::BEDFile("https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/genes/refGene.hg19.bed.gz") ## ----------------------------------------------------------------------------- epiviz_igv <- epiviz_env$plot( file1, datasource_name = "genes2", chr="chr11", start=118000000, end=121000000) epiviz_env