Genome arithmetics
In multicrispr: Multi-locus multi-purpose Crispr/Cas design

knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, cache = FALSE)
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Introduction {-}

This vignette discusses multicrispr's genome arithmetics functionality, often required in the first step of Crispr/Cas9 design. Multicrispr's genome arithmetics functions allow two-way transformations around a genomic range's start/end. The r Biocpkg("GenomicRanges") and r Biocpkg("plyranges") packages also offer an extensive genome arithmetics functionality, though with functions designed as one-way transformations.

We illustrate the different operations on a small GRanges with four prime editing targets in Anazlone et al. (2019)

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'))

Genome arithmetics {-}

Extend {-}

ext <- extend(gr, start = -10, end = +10, plot = TRUE)

Up flank {-}

up <- up_flank(gr,  -22,  -1, plot=TRUE, facet_var=c('targetname', 'seqnames'))

Down flank {-}

dn <- down_flank(gr, +1, +22, plot=TRUE)

Double flank {-}

dbl <- double_flank(gr, -10,  -1, +1, +20, plot = TRUE)

References {-}

Anzalone, A.V., Randolph, P.B., Davis, J.R. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019). https://doi.org/10.1038/s41586-019-1711-4