## ----include=TRUE, echo=FALSE, message=FALSE---------------------------------- knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, cache = FALSE) #str(knitr::opts_chunk$get()) ## ----fig.width=5.5, fig.height=3, out.width="85%"----------------------------- require(multicrispr) bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 gr <- char_to_granges(c(PRNP = 'chr20:4699600:+', # snp HBB = 'chr11:5227002:-', # snp HEXA = 'chr15:72346580-72346583:-', # del CFTR = 'chr7:117559593-117559595:+'),# ins bsgenome = bsgenome) plot_intervals(gr, facet_var = c('targetname','seqnames')) ## ----fig.width=5.5, fig.height=3, out.width="85%"----------------------------- ext <- extend(gr, start = -10, end = +10, plot = TRUE) ## ----fig.width=5.5, fig.height=3, out.width="85%"----------------------------- up <- up_flank(gr, -22, -1, plot=TRUE, facet_var=c('targetname', 'seqnames')) ## ----fig.width=5.5, fig.height=3, out.width="85%"----------------------------- dn <- down_flank(gr, +1, +22, plot=TRUE) ## ----fig.width=5.5, fig.height=3, out.width="85%"----------------------------- dbl <- double_flank(gr, -10, -1, +1, +20, plot = TRUE)