Nothing
## ---- 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)
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