Documented crisprai objects

.Rbuildignore

@@ -2,4 +2,5 @@ vignettes/figures/resave.sh
 vignettes/figures/*.pptx
 ^\.BBSoptions$
 inst/python/azimuth/azimuth/azure_models/*
-inst/crisprai
+inst/crisprai
+vignettes/crisprScore_paper*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: crisprScore
-Version: 1.1.15
-Date: 2022-07-23
+Version: 1.1.16
+Date: 2022-10-22
 Title: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
 Authors@R: c(
     person("Jean-Philippe", "Fortin", email = "[email protected]", role = c("aut", "cre", "cph")),
@@ -41,7 +41,7 @@ Description:
     Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines. 
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 VignetteBuilder: knitr
 StagedInstall: no
 BugReports: https://github.com/crisprVerse/crisprScore

R/data.R

@@ -1,61 +1,61 @@
-#' Mismatch position weights for the CFD off-target algorithm (Cas9)
-#'
-#' CFD off-target scoring weights for each nucleotide position and each
-#'     pair of DNA:RNA mismatches, for 20-mer spacer sequences.
-#'     Position 20 refers to the spacer position adjacent to
-#'     the PAM sequence. A higher weight indicates greater mismatch tolerance 
-#'     by the Cas9 nuclease.
-#' 
-#' @format Numeric vector 
-#' @source \url{https://dx.doi.org/10.1038\%2Fnbt.3437}
-"cfd.mm.weights.cas9"
+# #' Mismatch position weights for the CFD off-target algorithm (Cas9)
+# #'
+# #' CFD off-target scoring weights for each nucleotide position and each
+# #'     pair of DNA:RNA mismatches, for 20-mer spacer sequences.
+# #'     Position 20 refers to the spacer position adjacent to
+# #'     the PAM sequence. A higher weight indicates greater mismatch tolerance 
+# #'     by the Cas9 nuclease.
+# #' 
+# #' @format Numeric vector 
+# #' @source \url{https://dx.doi.org/10.1038\%2Fnbt.3437}
+# "cfd.mm.weights.cas9"
 
 
-#' PAM sequence weights for the CFD off-target algorithm (Cas9)
-#'
-#' CFD off-target PAM weights for each possible 3-mer Cas9 PAM sequences.
-#'     A higher weight indicates greater mismatch tolerance 
-#'     by the Cas9 nuclease.
-#' 
-#' @format Numeric vector
-#' @source \url{https://dx.doi.org/10.1038\%2Fnbt.3437}
-"cfd.pam.weights.cas9"
+# #' PAM sequence weights for the CFD off-target algorithm (Cas9)
+# #'
+# #' CFD off-target PAM weights for each possible 3-mer Cas9 PAM sequences.
+# #'     A higher weight indicates greater mismatch tolerance 
+# #'     by the Cas9 nuclease.
+# #' 
+# #' @format Numeric vector
+# #' @source \url{https://dx.doi.org/10.1038\%2Fnbt.3437}
+# "cfd.pam.weights.cas9"
 
 
-#' Mismatch position weights for the CFD off-target algorithm (CasRx)
-#'
-#' CFD off-target scoring weights for each nucleotide position and each
-#'     pair of DNA:RNA mismatches, for 27-mer spacer sequences.
-#'     Position 1 refers to the spacer position adjacent to
-#'     the PAM sequence. A higher weight indicates greater mismatch tolerance 
-#'     by the CasRx nuclease.
-#' 
-#' @format Numeric vector 
-"cfd.mm.weights.casrx"
+# #' Mismatch position weights for the CFD off-target algorithm (CasRx)
+# #'
+# #' CFD off-target scoring weights for each nucleotide position and each
+# #'     pair of DNA:RNA mismatches, for 27-mer spacer sequences.
+# #'     Position 1 refers to the spacer position adjacent to
+# #'     the PAM sequence. A higher weight indicates greater mismatch tolerance 
+# #'     by the CasRx nuclease.
+# #' 
+# #' @format Numeric vector 
+# "cfd.mm.weights.casrx"
 
 
-#' PAM sequence weights for the CFD off-target algorithm (CasRx)
-#'
-#' CFD off-target PAM weights for each possible 1-mer CasRx PAM sequences.
-#'     A higher weight indicates greater mismatch tolerance 
-#'     by the CasRx nuclease.
-#' 
-#' @format Numeric vector
-"cfd.pam.weights.casrx"
+# #' PAM sequence weights for the CFD off-target algorithm (CasRx)
+# #'
+# #' CFD off-target PAM weights for each possible 1-mer CasRx PAM sequences.
+# #'     A higher weight indicates greater mismatch tolerance 
+# #'     by the CasRx nuclease.
+# #' 
+# #' @format Numeric vector
+# "cfd.pam.weights.casrx"
 
 
 
 
-#' Mismatch position weights for the MIT off-target algorithm (Cas9)
-#'
-#' MIT off-target scoring weights for each nucleotide position, for 20-mer
-#'     spacer sequences. Position 20 refers to the spacer position adjacent to
-#'     the PAM sequence. A higher weight indicates greater mismatch tolerance 
-#'     by the Cas9 nuclease.
-#' 
-#' @format Numeric vector 
-#' @source \url{https://dx.doi.org/10.1038\%2Fnbt.2647}
-"mit.weights"
+# #' Mismatch position weights for the MIT off-target algorithm (Cas9)
+# #'
+# #' MIT off-target scoring weights for each nucleotide position, for 20-mer
+# #'     spacer sequences. Position 20 refers to the spacer position adjacent to
+# #'     the PAM sequence. A higher weight indicates greater mismatch tolerance 
+# #'     by the Cas9 nuclease.
+# #' 
+# #' @format Numeric vector 
+# #' @source \url{https://dx.doi.org/10.1038\%2Fnbt.2647}
+# "mit.weights"
 
 
 
@@ -78,5 +78,83 @@
 #' @usage data(scoringMethodsInfo)
 "scoringMethodsInfo"
 
-## To do: add documentation for sgrna and tss example files
+
+
+
+#' Example CRISPRa gRNAs data.frame for the getCrispraiScores function
+#'
+#' Example CRISPRa gRNAs data.frame for the getCrispraiScores function. 
+#'     The targeted TSSs are described in the object tssExampleCrispra.
+#' 
+#' @format A data.frame with 5 columns:
+#' \describe{
+#'   \item{grna_id}{String specifying gRNA unique identifier.}
+#'   \item{tss_id}{String specifying the targeted TSS id.}
+#'   \item{pam_site}{Genomic coordinate specifying the first nucleotide of 
+#'        PAM sequence.}
+#'   \item{strand}{Strand of the gRNA strand. Must be "+" or "-".}
+#'   \item{spacer_19mer}{String specifying the nucleotide sequence of the 19mer
+#'    spacer sequence.}
+#' }
+#' @usage data(sgrnaExampleCrispra)
+"sgrnaExampleCrispra"
+
+
+#' Example CRISPRi gRNAs data.frame for the getCrispraiScores function
+#'
+#' Example CRISPRi gRNAs data.frame for the getCrispraiScores function.
+#'     The targeted TSSs are described in the object tssExampleCrispri.
+#' 
+#' @format A data.frame with 5 columns:
+#' \describe{
+#'   \item{grna_id}{String specifying gRNA unique identifier.}
+#'   \item{tss_id}{String specifying the targeted TSS id.}
+#'   \item{pam_site}{Genomic coordinate specifying the first nucleotide of 
+#'        PAM sequence.}
+#'   \item{strand}{Strand of the gRNA strand. Must be "+" or "-".}
+#'   \item{spacer_19mer}{String specifying the nucleotide sequence of the 19mer
+#'    spacer sequence.}
+#' }
+#' @usage data(sgrnaExampleCrispri)
+"sgrnaExampleCrispri"
+
+
+
+#' Example TSS data.frame for the getCrispraiScores function
+#'
+#' Example TSS data for gRNAs stored in sgrnaExampleCrispra.
+#' 
+#' @format A data.frame with 7 columns:
+#' \describe{
+#'   \item{tss_id}{String specifying the targeted TSS id.}
+#'   \item{gene_symbol}{String specifying gene symbol.}
+#'   \item{promoter}{String specifying the promoter suffix to add to the
+#'   gene symbol columns to obtain the unique TSS id.}
+#'   \item{transcripts}{Ensembl IDs of the targeted transcript.}
+#'   \item{position}{Integer specifying genomic coordinate of the TSS.}
+#'   \item{strand}{Strand of TSS. Must be "+" or "-".}
+#'   \item{chr}{String specifying the chromosome name.}
+#' }
+#' @usage data(tssExampleCrispra)
+"tssExampleCrispra"
+
+
+#' Example TSS data.frame for the getCrispraiScores function
+#'
+#' Example TSS data for gRNAs stored in sgrnaExampleCrispri.
+#' 
+#' @format A data.frame with 7 columns:
+#' \describe{
+#'   \item{tss_id}{String specifying the targeted TSS id.}
+#'   \item{gene_symbol}{String specifying gene symbol.}
+#'   \item{promoter}{String specifying the promoter suffix to add to the
+#'   gene symbol columns to obtain the unique TSS id.}
+#'   \item{transcripts}{Ensembl IDs of the targeted transcript.}
+#'   \item{position}{Integer specifying genomic coordinate of the TSS.}
+#'   \item{strand}{Strand of TSS. Must be "+" or "-".}
+#'   \item{chr}{String specifying the chromosome name.}
+#' }
+#' @usage data(tssExampleCrispri)
+"tssExampleCrispri"
+
 

R/getCasRxRFScores.R

@@ -42,13 +42,13 @@
 #' 
 #' @examples
 #' 
-#' \donttest{
-#' fasta <- file.path(system.file(package="crisprScore"),
-#'     "casrxrf/test.fa")
-#' mrnaSequence <- Biostrings::readDNAStringSet(filepath=fasta,
-#'     format="fasta",
-#'     use.names=TRUE)
-#' results <- getCasRxRFScores(mrnaSequence)
+#' if (interactive()){
+#'     fasta <- file.path(system.file(package="crisprScore"),
+#'         "casrxrf/test.fa")
+#'     mrnaSequence <- Biostrings::readDNAStringSet(filepath=fasta,
+#'         format="fasta",
+#'         use.names=TRUE)
+#'     results <- getCasRxRFScores(mrnaSequence)
 #' }
 #' 
 #' @export