Package 'crisprBase'

Title: Base functions and classes for CRISPR gRNA design
Description: Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.
Authors: Jean-Philippe Fortin [aut, cre]
Maintainer: Jean-Philippe Fortin <[email protected]>
License: MIT + file LICENSE
Version: 1.11.0
Built: 2024-10-30 05:34:58 UTC
Source: https://github.com/bioc/crisprBase

Help Index

Annotate mismatches between spacer and protospacer sequences

Description

Annotate mismatches between spacer and protospacer sequences.

Usage

annotateMismatches(spacers, protospacers, rnase = FALSE)

Arguments

spacers

A character vector specifying spacer sequences (gRNA).
protospacers

A character vector specifying protospacer sequences (target DNA).
rnase

Is it for an RNAse? FALSE by default. If TRUE, spacers and protospacers are expected to be the reverse complement of each other.

Value

A data.frame storing spacer and protospacer columns, as well as number of mismatches, and positions for the different mismatches, if any. Positions are relative to the 5' end of the spacer sequences. For RNAses (e.g. CasRx), this means that a mismatch at position 1 corresponds to the last nucleotide of the protospacer sequence.

Author(s)

Jean-Philippe Fortin

Examples

spacers <- c("CCGGAGCGAGTTGCAGTAAGCAG",
    "GCCGGAGCGAGTTGCAGTAAGCA", 
    "GGCCGGAGCGAGTTGCAGTAAGC")

protospacers=c("CTGCTTACTGCAACTCGCTCTGG",
    "TGCTTAATGCAACCCGCTCCGGC", 
    "GCTTACTGCAACTCGCTCCGGCC")

ann <- annotateMismatches(spacers,
    protospacers,
    rnase=TRUE)

AsCas12a CrisprNuclease object

Description

CrisprNuclease object for the Wildtype Acidaminococcus Cas12a (AsCas12a) nuclease.

Usage

data(AsCas12a, package="crisprBase")

Format

CrisprNuclease object.

Details

The AsCas12a nuclease recognizes TTTV PAM sequences. Spacer sequences must be located downstream of PAM sequences.

An S4 class to represent a base editor

Description

An S4 class to represent a base editor

Usage

baseEditorName(object)

baseEditorName(object) <- value

editingWeights(object, ...)

editingWeights(object) <- value

editingStrand(object, ...)

editingStrand(object) <- value

BaseEditor(
  CrisprNuclease,
  baseEditorName = NA_character_,
  editingStrand = c("original", "opposite"),
  editingWeights = NULL
)

## S4 method for signature 'BaseEditor'
show(object)

## S4 method for signature 'BaseEditor'
baseEditorName(object)

## S4 replacement method for signature 'BaseEditor'
baseEditorName(object) <- value

## S4 method for signature 'BaseEditor'
editingWeights(object, substitutions = NULL)

## S4 replacement method for signature 'BaseEditor'
editingWeights(object) <- value

## S4 method for signature 'BaseEditor'
editingStrand(object)

## S4 replacement method for signature 'BaseEditor'
editingStrand(object) <- value

Arguments

object

BaseEditor object.
value

Value to replaced with.
...

Additional arguments for class-specific methods
CrisprNuclease

A CrisprNuclease object.
baseEditorName

String specifying base editor name.
editingStrand

String indicating which strand with respect to the target protospacer sequence will be edited. Must be either "original" or "opposite". "original" by default.
editingWeights

Numeric matrix of editing weights. Column names must be indicating relative position to the PAM site. Row names must be of the form "X2Y" where "X" represents the origin base, and "Y" represents the subtituted base. For instance, "C2T" indicates the row corresponding to C to T editing.
substitutions

Character vector indicating which substitutions should be returned.

Value

A BaseEditor object

Functions

Slots

baseEditorName

Name of the base editor.

editingWeights

Matrix of editing weights.

editingStrand

String indicating which strand with respect to the target protospacer sequence will be edited. Must be either "original" or "opposite". "original" by default.

Constructors

Use the constructor link{BaseEditor} to create a BaseEditor object.

Accessors

baseEditorName:

To get the name of the base editor.

editingWeights:

To return the matrix of editing weights.

editingStrand:

To return the editing strand.

Setters

baseEditorName<-:

To change the name of the base editor.

editingWeights<-:

To change the matrix of editing weights.

editingStrand<-:

To change the editing strand.

Examples

# Creating an object for BE4max (C to T editor)
# based on experimental weights

ws <- c(0.7, 0.7, 0.8, 1.8, 1, 2, 1.4, 1.2, 2.3, 1.3, 2.4, 2.2, 3.4, 
      2.2, 2.1, 3.5, 5.8, 16.2, 31.8, 63.2, 90.3, 100, 87, 62, 31.4, 
      16.3, 10, 5.6, 3.3, 1.9, 1.8, 2.4, 1.7, 0.5, 0.2, 0.1)
ws <- matrix(ws, nrow=1, ncol=length(ws))
rownames(ws) <- "C2T"
colnames(ws) <- -36:-1
data(SpCas9, package="crisprBase")
BE4max <- BaseEditor(SpCas9,
                     baseEditorName="BE4max",
                     editingStrand="original",
                     editingWeights=ws)
metadata(BE4max)$description_base_editor <- "BE4max cytosine base editor."

BE4max BaseEditor object

Description

BaseEditor for the cytosine base editor CRISPR/Cas9 system BE4max. Editing weights were obtained from https://doi.org/10.1016/j.cell.2020.05.037

Usage

data(BE4max, package="crisprBase")

Format

BaseEditor object.

Details

BaseEditor for the cytosine base editor CRISPR/Cas9 system BE4max. Editing weights were obtained from https://doi.org/10.1016/j.cell.2020.05.037.

CasRx CrisprNuclease object

Description

CrisprNuclease object for the Cas13d-NLS from Ruminococcus flavefaciens strain XPD3002 nuclease (RNase).

Usage

data(CasRx, package="crisprBase")

Format

CrisprNuclease object.

Details

The CasRx nuclease was derived from Cas13d Ruminococcus flavefaciens string XPD3002. See 10.1016/j.cell.2018.02.033.

An S4 class to represent a CRISPR nickase.

Description

An S4 class to represent a CRISPR nickase.

Usage

CrisprNickase(
  nickaseName,
  nickingStrand = c("original", "opposite"),
  pams = NA_character_,
  weights = rep(1, length(pams)),
  metadata = list(),
  pam_side = NA_character_,
  spacer_gap = 0L,
  spacer_length = NA_integer_
)

## S4 method for signature 'CrisprNickase'
show(object)

## S4 method for signature 'CrisprNickase'
pamLength(object)

## S4 method for signature 'CrisprNickase'
spacerLength(object)

## S4 replacement method for signature 'CrisprNickase'
spacerLength(object) <- value

## S4 method for signature 'CrisprNickase'
pamSide(object)

## S4 replacement method for signature 'CrisprNickase'
pamSide(object) <- value

## S4 method for signature 'CrisprNickase'
spacerGap(object)

## S4 replacement method for signature 'CrisprNickase'
spacerGap(object) <- value

## S4 method for signature 'CrisprNickase'
hasSpacerGap(object)

## S4 method for signature 'CrisprNickase'
targetLength(object)

## S4 method for signature 'CrisprNickase'
pams(object, primary = TRUE, ignore_pam = FALSE, as.character = FALSE)

## S4 method for signature 'CrisprNickase'
pamIndices(object)

## S4 method for signature 'CrisprNickase'
spacerIndices(object)

## S4 method for signature 'CrisprNickase'
prototypeSequence(object, primary = TRUE)

Arguments

nickaseName

Name of the CRISPR nickase.
nickingStrand

String specifying with strand with respect to the motif sequence (5' to 3') is nicked. Must be either "original" (default) or "opposite".
pams

Character vector of PAM sequence motifs written from 5' to 3. If the point of cleavage has been determined, the precise site is marked with ^. Only letters in the IUPAC code are accepted. For nickases that cleave away from their recognition sequence, the cleavage sites are indicated in parentheses. See details for more information.
weights

Optional numeric vector specifying relative weights of the PAM sequences to specify cleavage probabilities.
metadata

Optional list providing global metadata information.
pam_side

String specifying the side of the PAM sequence sequence with respect to the protospacer sequence. Must be either '3prime' (e.g. Cas9) or '5prime' (e.g. Cas12a)
spacer_gap

Integer specifying the length (in nucleotides) between the spacer sequence and the PAM sequence (e.g. 0 for Cas9 and Cas12a).
spacer_length

Integer specifying the length of the spacer sequence
object

CrisprNickase object.
value

For spacerLength<- and gapLength<-, must be a non-negative integer. For pamSide, must be either '5prime' or '3prime'.
primary

Should only the PAM sequence with the heighest weight be returned? If no cleavage weights are stored in the CrisprNickase object, all sequences are returned. TRUE by default.
ignore_pam

Should all possible k-mer sequences for a given PAM length be returned, irrespetively of the PAM sequence motifs stored in the CrisprNickase object? FALSE by default.
as.character

Should the PAM sequences be returned as a character vector? FALSE by default.

Value

A CrisprNickase object

Functions

Slots

pam_side

String specifying the side of the PAM sequence with respect to the protospacer sequence. Must be either '3prime' (e.g. SpCas9) or '5prime' (e.g. AsCas12a)

spacer_length

Integer specifying the length of the spacer sequence

spacer_gap

Integer specifying the length (in nucleotides) between the spacer sequence and the PAM sequence (e.g. 0 for SpCas9 and AsCas12a).

Constructors

Use the constructor link{CrisprNickase} to create a CrisprNickase object.

Accessors

nickaseName:

To get the name of the CRISPR nickase.

spacerLength:

To return the length of the spacer sequence.

targetLength:

To return the length of the target sequence (protospacer + pam).

pamLength:

To return the length of the PAM sequence.

pamSide:

To return the side of the PAM sequence with respect to the spacer sequence.

spacerGap:

To return the length of the gap between the PAM and spacer sequences.

pams:

To return the list of PAM sequences.

Setters

spacerGap<-:

To change the length of the gap between the PAM and spacer sequences.

pamSide<-:

To change the side of the PAM sequence with respect to the protospacer sequence.

spacerLength<-:

To change the length of the spacer sequence.

Utility functions for genomic arithmetics

pamIndices:

To return the relative coordinates of the PAM sequence within the protospacer sequence.

spacerIndices:

To return the relatiive coordinates of the spacer sequence within the protospacer sequence.

Examples

Cas9D10A <- CrisprNickase("Cas9D10A",
                          nickingStrand="opposite",
                          pams=c("(3)NGG", "(3)NAG", "(3)NGA"),
                          weights=c(1, 0.2593, 0.0694),
                          metadata=list(description="D10A-mutated  Streptococcus
                                        pyogenes Cas9 (SpCas9) nickase"),
                          pam_side="3prime",
                          spacer_length=20)

Cas9H840A <- CrisprNickase("Cas9H840A",
                           nickingStrand="original",
                           pams=c("(3)NGG", "(3)NAG", "(3)NGA"),
                           weights=c(1, 0.2593, 0.0694),
                           metadata=list(description="H840A-mutated  Streptococcus
                                         pyogenes Cas9 (SpCas9) nickase"),
                           pam_side="3prime",
                           spacer_length=20)

Csm CrisprNuclease object

Description

CrisprNuclease object for the RNA-targeting Csm complex from Streptococcus thermophilus

Usage

data(Csm, package="crisprBase")

Format

CrisprNuclease object.

Details

The specific Csm complex is an RNA-targeting nuclease derived from Streptococcus thermophilus. There is no preferred PAM sequences, and the default (optimal) spacer length is 32nt. See https://doi.org/10.1038/s41587-022-01649-9.

enAsCas12a CrisprNuclease object

Description

CrisprNuclease object for the Enhanced Acidaminococcus Cas12a (AsCas12a) nuclease.

Usage

data(enAsCas12a, package="crisprBase")

Format

CrisprNuclease object.

Details

The enAsCas12a nuclease recognizes an extended set of PAM sequences beyong the canonical TTTV sequence for AsCas12a. Spacer sequences must be located downstream of PAM sequences.

Extract PAM sequences from target sequences

Description

Extract PAM sequences from target sequences (protospacer + PAM) using information stored in a CrisprNuclease object.

Usage

extractPamFromTarget(targets, object)

Arguments

targets

Character vector of target sequences.
object

CrisprNuclease corresponding to the target sequences.

Value

Character vector of PAM sequences of length equal to that of the targets character vector.

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, AsCas12a, package="crisprBase")
# Extracting PAM sequences from Cas9 protospacers:
targets <- c("AGGTGCTGATTGTAGTGCTGCGG",
              "AGGTGCTGATTGTAGTGCTGAGG")
extractPamFromTarget(targets, SpCas9)
# Extracting PAM sequences from Cas12a targets:
targets <- c("TTTAAGGTGCTGATTGTAGTGCTGTGT",
             "TTTCAGGTGCTGATTGTAGTGCTGAAA")
extractPamFromTarget(targets, AsCas12a)

Extract protospacer sequences from target sequences

Description

Extract protospacer sequences from target sequences (protospacer + PAM) using information stored in a CrisprNuclease object.

Usage

extractProtospacerFromTarget(targets, object)

Arguments

targets

Character vector of targets sequences.
object

CrisprNuclease corresponding to the targets sequences.

Value

Character vector of protospacer sequences of length equal to that of the targets character vector.

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, AsCas12a, package="crisprBase")
# Extracting protospacer sequences from Cas9 targets:
targets <- c("AGGTGCTGATTGTAGTGCTGCGG",
             "AGGTGCTGATTGTAGTGCTGAGG")
extractProtospacerFromTarget(targets, SpCas9)
# Extracting protospacer sequences from Cas12a targets:
targets <- c("TTTAAGGTGCTGATTGTAGTGCTGTGT",
             "TTTCAGGTGCTGATTGTAGTGCTGAAA")
extractProtospacerFromTarget(targets, AsCas12a)

Return list of available CrisprNuclease objects in crisprBase

Description

Return list of available CrisprNuclease objects in crisprBase.

Usage

getAvailableCrisprNucleases()

Value

Character vector of available CrisprNuclease objects found in crisprBase.

Author(s)

Jean-Philippe Fortin

Examples

getAvailableCrisprNucleases()

Return cut site coordinates from PAM site coordinates

Description

Return cut site coordinates from PAM site coordinates.

Usage

getCutSiteFromPamSite(pam_site, strand, nuclease = NULL)

Arguments

pam_site

Coordinate of the first nucleotide of the PAM sequence.
strand

Either "+" or "-".
nuclease

A CrisprNuclease object.

Value

numeric vector of cut sites

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, package="crisprBase")
getCutSiteFromPamSite(pam_site=100, strand="+", nuclease=SpCas9)
getCutSiteFromPamSite(pam_site=100, strand="-", nuclease=SpCas9)

Construct a cut site GRanges from a list of PAM sites

Description

Construct a cut site GRanges from a list of PAM sites using information stored in a CrisprNuclease object.

Usage

getCutSiteRanges(
  gr = NULL,
  seqnames = NULL,
  pam_site = NULL,
  strand = NULL,
  nuclease = NULL
)

Arguments

gr

GRanges object of width 1 specifying the coordinates of the first nucleotide of the PAM sequences.
seqnames

Character vector of genomic sequence names. Ignored if gr is not NULL.
pam_site

Numeric vector specifying the coordinates of the first nucleotide of the PAM sequences corresponding to the PAM sequences. Ignored if gr is not NULL.
strand

Character vector specifying the strand of the PAM. Ignored if gr is not NULL.
nuclease

CrisprNuclease object.

Value

GRanges object representing genomic coordinates of the cut sites.

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, AsCas12a, package="crisprBase")
library(GenomicRanges)
gr <- GRanges("chr10",
              IRanges(start=c(100,120), width=1),
              strand=c("+","-"))
getCutSiteRanges(gr, nuclease=SpCas9)
getCutSiteRanges(gr, nuclease=AsCas12a)

Return optimal editing site coordinates from PAM site coordinates

Description

Return optimal editing site coordinates from PAM site coordinates.

Usage

getEditingSiteFromPamSite(
  pam_site,
  strand,
  baseEditor = NULL,
  substitution = NULL
)

Arguments

pam_site

Coordinate of the first nucleotide of the PAM sequence.
strand

Either "+" or "-".
baseEditor

A BaseEditor object.
substitution

String indicating which substitution should be used to estimate the optimal editing position. E.g. "C2T" will return the optimal editing position for C to T editing.

Value

numeric vector of editing sites.

Author(s)

Jean-Philippe Fortin

Examples

data(BE4max, package="crisprBase")
getEditingSiteFromPamSite(pam_site=100, strand="+", baseEditor=BE4max, "C2T")

Construct a PAM GRanges from a list of PAM sites

Description

Construct a PAM GRanges from a list of PAM sites using information stored in a CrisprNuclease object.

Usage

getPamRanges(
  gr = NULL,
  seqnames = NULL,
  pam_site = NULL,
  strand = NULL,
  nuclease = NULL
)

Arguments

gr

GRanges object of width 1 specifying the coordinates of the first nucleotide of the PAM sequences.
seqnames

Character vector of genomic sequence names. Ignored if gr is not NULL.
pam_site

Numeric vector specifying the coordinates of the first nucleotide of the PAM sequences corresponding to the PAM sequences. Ignored if gr is not NULL.
strand

Character vector specifying the strand of the PAM. Ignored if gr is not NULL.
nuclease

CrisprNuclease object.

Value

GRanges object representing genomic coordinates of PAM sequences.

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, AsCas12a, package="crisprBase")
library(GenomicRanges)
gr <- GRanges("chr10",
              IRanges(start=c(100,120), width=1),
              strand=c("+","-"))
getPamRanges(gr, nuclease=SpCas9)
getPamRanges(gr, nuclease=AsCas12a)

Construct a protospacer GRanges from a list of PAM sites

Description

Construct a protospacer GRanges from a list of PAM sites using information stored in a CrisprNuclease object.

Usage

getProtospacerRanges(
  gr = NULL,
  seqnames = NULL,
  pam_site = NULL,
  strand = NULL,
  nuclease = NULL,
  spacer_len = NULL
)

Arguments

gr

GRanges object of width 1 specifying the coordinates of the first nucleotide of the PAM sequences.
seqnames

Character vector of genomic sequence names. Ignored if gr is not NULL.
pam_site

Numeric vector specifying the coordinates of the first nucleotide of the PAM sequences corresponding to the protospacers. Ignored if gr is not NULL.
strand

Character vector specifying the strand of the protospacer. Ignored if gr is not NULL.
nuclease

CrisprNuclease object.
spacer_len

Non-negative integer to overwrite the default spacer length stored in the CrisprNuclease object. s

Value

GRanges object representing genomic coordinates of protospacer sequences.

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, AsCas12a, package="crisprBase")
library(GenomicRanges)
gr <- GRanges("chr10",
              IRanges(start=c(100,120), width=1),
              strand=c("+","-"))
getProtospacerRanges(gr, nuclease=SpCas9)
getProtospacerRanges(gr, nuclease=AsCas12a)

Construct a target GRanges from a list of PAM sites

Description

Construct a target (protospacer + PAM) GRanges from a list of PAM sites using information stored in a CrisprNuclease object.

Usage

getTargetRanges(
  gr = NULL,
  seqnames = NULL,
  pam_site = NULL,
  strand = NULL,
  nuclease = NULL,
  spacer_len = NULL
)

Arguments

gr

GRanges object of width 1 specifying the coordinates of the first nucleotide of the PAM sequences.
seqnames

Character vector of genomic sequence names. Ignored if gr is not NULL.
pam_site

Numeric vector specifying the coordinates of the first nucleotide of the PAM sequences corresponding to the targets. Ignored if gr is not NULL.
strand

Character vector specifying the strand of the target. Ignored if gr is not NULL.
nuclease

CrisprNuclease object.
spacer_len

Non-negative integer to overwrite the default spacer length stored in the CrisprNuclease object.

Value

GRanges object representing genomic coordinates of the target sequences.

Author(s)

Jean-Philippe Fortin

Examples

data(SpCas9, AsCas12a, package="crisprBase")
library(GenomicRanges)
gr <- GRanges("chr10",
              IRanges(start=c(100,120), width=1),
              strand=c("+","-"))
getTargetRanges(gr, nuclease=SpCas9)
getTargetRanges(gr, nuclease=AsCas12a)

MAD7 CrisprNuclease object

Description

CrisprNuclease object for the MAD7 nuclease (Cas12a-like nuclease)

Usage

data(MAD7, package="crisprBase")

Format

CrisprNuclease object.

Details

The MAD7 nuclease recognizes YTTV PAM sequences. Spacer sequences must be located downstream of PAM sequences.

An S4 class to represent a nuclease.

Description

Return motif string representations of recognition sites.

Return length of the recognition sites sequences.

Usage

motifs(object, ...)

motifLength(object, ...)

nucleaseName(object)

targetType(object)

weights(object, ...)

nucleaseName(object) <- value

targetType(object) <- value

weights(object) <- value

cutSites(object, ...)

isCutting(object)

isRnase(object)

isDnase(object)

Nuclease(
  nucleaseName,
  targetType = c("DNA", "RNA"),
  motifs = NULL,
  cutSites = NULL,
  weights = rep(1, length(motifs)),
  metadata = list()
)

## S4 method for signature 'Nuclease'
show(object)

## S4 method for signature 'Nuclease'
nucleaseName(object)

## S4 replacement method for signature 'Nuclease'
nucleaseName(object) <- value

## S4 method for signature 'Nuclease'
targetType(object)

## S4 replacement method for signature 'Nuclease'
targetType(object) <- value

## S4 method for signature 'Nuclease'
weights(object, expand = FALSE)

## S4 replacement method for signature 'Nuclease'
weights(object) <- value

## S4 method for signature 'Nuclease'
isCutting(object)

## S4 method for signature 'Nuclease'
isRnase(object)

## S4 method for signature 'Nuclease'
isDnase(object)

## S4 method for signature 'Nuclease'
motifs(
  object,
  primary = FALSE,
  strand = c("+", "-"),
  expand = FALSE,
  as.character = FALSE
)

## S4 method for signature 'Nuclease'
motifLength(object)

## S4 method for signature 'Nuclease'
cutSites(object, strand = c("+", "-", "both"), combine = TRUE, middle = FALSE)

Arguments

object

Nuclease object.
...

Additional arguments for class-specific methods
value

New value to pass to the setter functions.
nucleaseName

Name of the nuclease.
targetType

String specifying target type ("DNA" or "RNA").
motifs

Character vector of recognition sequence motifs written from 5' to 3' written in Rebase convention. If the point of cleavage has been determined, the precise site is marked with ^. Only letters in the IUPAC code are accepted. For nucleases that cleave away from their recognition sequence, the cleavage sites are indicated in parentheses. See details for more information.
cutSites

Matrix with 2 rows (+ and - strand, respectively) specifying the cleavage coordinates relative to the first nucleotide of the motif sequence. Each column corresponds to a motif specified in the motifs slot.
weights

Optional numeric vector specifying relative weights for the recognition motifs to specify cleavage probabilities.
metadata

Optional list providing global metadata information.
expand

Should sequences be expanded to only contain ATCG nucleotides? FALSE by default.
primary

Should only the motif with the highest weight be returned? FALSE by default. Only relevant if weights are stored in the Nuclease object.
strand

Strand to allow reverse complementation of the motif. "+" by default.
as.character

Should the motif sequences be returned as a character vector? FALSE by default.
combine

Should only unique values be considered? TRUE by default.
middle

For staggered cuts, should the middle point between the cut on the forward strand and the cut on the reverse strand be considered as the cut site? FALSE by default.

Value

A Nuclease object

Functions

Slots

nucleaseName

Name of the nuclease.

targetType

Character string indicationg target type ("DNA" or "RNA").

motifs

DNAStringSet of recognition sequence motifs written from 5' to 3'.

cutSites

Matrix with 2 rows (+ and - strand, respectively) specifying the cleavage coordinates relative to the first nucleotide of the motif sequence. Each column corresponds to a motif specified in the motifs slot.

weights

Optional numeric vector specifying relative weights for the motifs corresponding to cleavage probabilities.

metadata

Optional string providing a description of the nuclease.

Constructors

Use the constructor link{Nuclease} to create a Nuclease object.

Accessors

nucleaseName:

To get the name of the nuclease.

targetType:

To get the target type ("DNA" or "RNA").

metadata:

To get the metadata list of the nuclease.

motifs:

To get the recognition mofif nucleotide sequences.

weights:

To get nuclease weights.

cutSites:

To get nuclease cut sites.

See Also

See the CrisprNuclease for CRISPR-specific nucleases.

Examples

EcoRI <- Nuclease("EcoRI",
                  motifs=c("G^AATTC"),
                  metadata=list(description="EcoRI restriction enzyme"))

An S4 class to represent a nickase

Description

An S4 class to represent a nickase

Usage

nickaseName(object)

nickaseName(object) <- value

nickingStrand(object)

nickingStrand(object) <- value

Nickase(
  nickaseName,
  nickingStrand = c("original", "opposite"),
  motifs = NULL,
  cutSites = NULL,
  weights = rep(1, length(motifs)),
  metadata = list()
)

## S4 method for signature 'Nickase'
show(object)

## S4 method for signature 'Nickase'
nickaseName(object)

## S4 replacement method for signature 'Nickase'
nickaseName(object) <- value

## S4 method for signature 'Nickase'
nickingStrand(object)

## S4 replacement method for signature 'Nickase'
nickingStrand(object) <- value

## S4 method for signature 'Nickase'
weights(object, expand = FALSE)

## S4 replacement method for signature 'Nickase'
weights(object) <- value

## S4 method for signature 'Nickase'
isCutting(object)

## S4 method for signature 'Nickase'
motifs(
  object,
  primary = FALSE,
  strand = c("+", "-"),
  expand = FALSE,
  as.character = FALSE
)

## S4 method for signature 'Nickase'
motifLength(object)

## S4 method for signature 'Nickase'
cutSites(object, combine = TRUE)

Arguments

object

Nickase object.
value

New value to pass to the setter functions.
nickaseName

Name of the nickase.
nickingStrand

String specifying with strand with respect to the motif sequence (5' to 3') is nicked. Must be either "original" (default) or "opposite".
motifs

Character vector of recognition sequence motifs written from 5' to 3' written in Rebase convention. If the point of cleavage has been determined, the precise site is marked with ^. Only letters in the IUPAC code are accepted. For nickases that cleave away from their recognition sequence, the cleavage sites are indicated in parentheses. See details for more information.
cutSites

Vector specifying the cleavage coordinates relative to the first nucleotide of the motif sequence. Each column corresponds to a motif specified in the motifs slot.
weights

Optional numeric vector specifying relative weights for the recognition motifs to specify cleavage probabilities.
metadata

Optional list providing global metadata information.
expand

Should sequences be expanded to only contain ATCG nucleotides? FALSE by default.
primary

Should only the motif with the highest weight be returned? FALSE by default. Only relevant if weights are stored in the Nickase object.
strand

Strand to allow reverse complementation of the motif. "+" by default.
as.character

Should the motif sequences be returned as a character vector? FALSE by default.
combine

Should only unique values be considered? TRUE by default.

Value

A Nickase object

Functions

  • Nickase(): Create a Nickase object

Slots

nickaseName

Name of the nickase

motifs

DNAStringSet of recognition sequence motifs written from 5' to 3'.

nickingStrand

String specifying with strand with respect to the motif sequence (5' to 3') is nicked. Must be either "original" (default) or "opposite".

cutSites

Vector specifying the cleavage coordinates relative to the first nucleotide of the motif sequence. Each column corresponds to a motif specified in the motifs slot.

weights

Optional numeric vector specifying relative weights for the motifs corresponding to cleavage probabilities.

metadata

Optional string providing a description of the nickase.

Constructors

Use the constructor link{Nickase} to create a Nickase object.

Accessors

nickaseName:

To get the name of the nickase.

nickingStrand:

To get the nicking strand.

metadata:

To get the metadata list of the nickase

motifs:

To get the recognition mofif nucleotide sequences.

weights:

To get nickase weights.

cutSites:

To get nickase cut sites.

See Also

See the CrisprNickase for CRISPR-specific nickases.

Examples

Nb.BsmI <- Nickase("Nb.BsmI",
                   motifs=c("GAATG^C"),
                   nickingStrand="opposite",
                   metadata=list(description="Nb.BsmI nicking enzyme."))

Quick plot to visualize editing weights

Description

Quick plot to visualize editing weights from a BaseEditor object.

Usage

plotEditingWeights(
  baseEditor,
  discardEmptyRows = TRUE,
  substitutions = NULL,
  ...
)

Arguments

baseEditor

A BaseEditor object.
discardEmptyRows

Should rows that have all weight equal to 0 be discarded? TRUE by default.
substitutions

Character vector specifying substitutions to be plotted. If NULL (default), all substitutions are shown.
...

Additional arguments to be passed to plot

Value

Nothing. A plot is generated as a side effect.

Examples

if (interactive()){
    data(BE4max, package="crisprBase")
    plotEditingWeights(BE4max)
}

List of Nuclease objects representing common restriction enzymes

Description

List of Nuclease objects representing common restriction enzymes from REBASE database.

Usage

data(restrictionEnzymes, package="crisprBase")

Format

List of Nuclease objects.

Details

List of Nuclease objects representing common restriction enzymes from REBASE database.

SaCas9 CrisprNuclease object

Description

CrisprNuclease object for the wildtype Staphylococcus aureus Cas9 (SaCas9) nuclease.

Usage

data(SaCas9, package="crisprBase")

Format

CrisprNuclease object.

Details

The AsCas9 nuclease recognizes NNGRRT PAM sequences. Spacer sequences must be located upstream of PAM sequences. Editing weights were obtained from doi:10.1038/nature14299.

An S4 class to represent a CRISPR nuclease.

Description

An S4 class to represent a CRISPR nuclease.

Usage

spacerLength(object, ...)

targetLength(object, ...)

pamLength(object, ...)

spacerGap(object)

hasSpacerGap(object)

spacerGap(object) <- value

spacerLength(object) <- value

pamSide(object, ...)

pamSide(object) <- value

pams(object, ...)

pamIndices(object, ...)

spacerIndices(object, ...)

prototypeSequence(object, ...)

CrisprNuclease(
  nucleaseName,
  targetType = c("DNA", "RNA"),
  pams = NA_character_,
  weights = rep(1, length(pams)),
  metadata = list(),
  pam_side = NA_character_,
  spacer_gap = 0L,
  spacer_length = NA_integer_
)

## S4 method for signature 'CrisprNuclease'
show(object)

## S4 method for signature 'CrisprNuclease'
pamLength(object)

## S4 method for signature 'CrisprNuclease'
spacerLength(object)

## S4 replacement method for signature 'CrisprNuclease'
spacerLength(object) <- value

## S4 method for signature 'CrisprNuclease'
pamSide(object)

## S4 replacement method for signature 'CrisprNuclease'
pamSide(object) <- value

## S4 method for signature 'CrisprNuclease'
spacerGap(object)

## S4 replacement method for signature 'CrisprNuclease'
spacerGap(object) <- value

## S4 method for signature 'CrisprNuclease'
hasSpacerGap(object)

## S4 method for signature 'CrisprNuclease'
targetLength(object)

## S4 method for signature 'CrisprNuclease'
pams(object, primary = TRUE, ignore_pam = FALSE, as.character = FALSE)

## S4 method for signature 'CrisprNuclease'
pamIndices(object)

## S4 method for signature 'CrisprNuclease'
spacerIndices(object)

## S4 method for signature 'CrisprNuclease'
prototypeSequence(object, primary = TRUE)

Arguments

object

CrisprNuclease object.
...

Additional arguments for class-specific methods
value

For spacerLength<- and gapLength<-, must be a non-negative integer. For pamSide, must be either '5prime' or '3prime'.
nucleaseName

Name of the CRISPR nuclease.
targetType

String specifying target type ("DNA" or "RNA").
pams

Character vector of PAM sequence motifs written from 5' to 3. If the point of cleavage has been determined, the precise site is marked with ^. Only letters in the IUPAC code are accepted. For nucleases that cleave away from their recognition sequence, the cleavage sites are indicated in parentheses. See details for more information.
weights

Optional numeric vector specifying relative weights of the PAM sequences to specify cleavage probabilities.
metadata

Optional list providing global metadata information.
pam_side

String specifying the side of the PAM sequence sequence with respect to the protospacer sequence. Must be either '3prime' (e.g. Cas9) or '5prime' (e.g. Cas12a)
spacer_gap

Integer specifying the length (in nucleotides) between the spacer sequence and the PAM sequence (e.g. 0 for Cas9 and Cas12a).
spacer_length

Integer specifying the length of the spacer sequence
primary

Should only the PAM sequence with the heighest weight be returned? If no cleavage weights are stored in the CrisprNuclease object, all sequences are returned. TRUE by default.
ignore_pam

Should all possible k-mer sequences for a given PAM length be returned, irrespetively of the PAM sequence motifs stored in the CrisprNuclease object? FALSE by default.
as.character

Should the PAM sequences be returned as a character vector? FALSE by default.

Value

A CrisprNuclease object

Functions

Slots

pam_side

String specifying the side of the PAM sequence with respect to the protospacer sequence. Must be either '3prime' (e.g. SpCas9) or '5prime' (e.g. AsCas12a)

spacer_length

Integer specifying the length of the spacer sequence

spacer_gap

Integer specifying the length (in nucleotides) between the spacer sequence and the PAM sequence (e.g. 0 for SpCas9 and AsCas12a).

Constructors

Use the constructor link{CrisprNuclease} to create a CrisprNuclease object.

Accessors

nucleaseName:

To get the name of the CRISPR nuclease.

spacerLength:

To return the length of the spacer sequence.

targetLength:

To return the length of the target sequence (protospacer + pam).

pamLength:

To return the length of the PAM sequence.

pamSide:

To return the side of the PAM sequence with respect to the spacer sequence.

spacerGap:

To return the length of the gap between the PAM and spacer sequences.

pams:

To return the list of PAM sequences.

Setters

spacerGap<-:

To change the length of the gap between the PAM and spacer sequences.

pamSide<-:

To change the side of the PAM sequence with respect to the protospacer sequence.

spacerLength<-:

To change the length of the spacer sequence.

Utility functions for genomic arithmetics

pamIndices:

To return the relative coordinates of the PAM sequence within the target sequence.

spacerIndices:

To return the relatiive coordinates of the spacer sequence within the target sequence.

Examples

SpCas9 <- CrisprNuclease("SpCas9",
                         pams=c("(3/3)NGG", "(3/3)NAG", "(3/3)NGA"),
                         weights=c(1, 0.2593, 0.0694),
                         metadata=list(description="Wildtype Streptococcus
                                       pyogenes Cas9 (SpCas9) nuclease"),
                         pam_side="3prime",
                         spacer_length=20)

SpCas9 CrisprNuclease object

Description

CrisprNuclease object for the wildtype Streptococcus pyogenes Cas9 (SpCas9) nuclease.

Usage

data(SpCas9, package="crisprBase")

Format

CrisprNuclease object.

Details

The SpCas9 nuclease recognizes NGG PAM sequences. Spacer sequences must be located upstream of PAM sequences.

SpGCas9 CrisprNuclease object

Description

CrisprNuclease object for the engineered Streptococcus pyogenes Cas9 SpG nuclease.

Usage

data(SpGCas9, package="crisprBase")

Format

CrisprNuclease object.

Details

The SpGCas9 nuclease recognizes NGN PAM sequences. Spacer sequences must be located upstream of PAM sequences.