getCrisprGuides: Retrieve CRISPR/Cas9 guides.

In RareVariantVis: A suite for analysis of rare genomic variants in whole genome sequencing data

Description

Function checks whether a guideRNA can be found that overlaps given SNP. Returns sequence of the guideRNA with the variant marked with the lowercase letters. When multiple guideRNAs are possible for given SNP, guideRNA with the variant closest to the PAM site is being selected.

Arguments

df	A data frame, preferably out from chromosomeVis.
genome	A object of the BSGenome, by default BSgenome.Hsapiens.UCSC.hg19.
gsize	Prefered size of the guideRNA, by default, standard 23 is used.
PAM	Prefered Protospacer Adjecent Motif "PAM", short motif that has to be found on the 5' end of the guideRNA, by default, Cas9 is used "GG".
PAM_rev	Prefered Protospacer Adjecent Motif "PAM", short motif that has to be found on the reverse strand, by default, Cas9 is used "CC". This is checked only when no guideRNA is found on the forward strand.

Value

character vector

Vector of guideRNAs, when no guideRNA was found for the forward strand, reverse strand is checked, when no guideRNA is found NA is returned.

Author(s)

Kornel Labun

Examples

file <- system.file("extdata", "RareVariants_CoriellIndex_S1.txt",
    package = "RareVariantVis")
df <- read.delim(file, stringsAsFactors = FALSE)
getCrisprGuides(df)

RareVariantVis documentation built on Nov. 8, 2020, 11:08 p.m.