add_genome_matches / add_target_matches: export & optionalize

DESCRIPTION

 Package: multicrispr
 Title: Multi-locus multi-purpose Crispr/Cas design 
-Version: 0.99.29
+Version: 0.99.30
 Authors@R: c(person("Aditya",   "Bhagwat",    NULL, "aditya.bhagwat@mpi-bn.mpg.de",   c("aut", "cre")),
             person( "Johannes", "Graumann",   NULL, 'johannes.graumann@mpi-bn.mpg.de',c("sad", "ctb")),
             person( "Mette",    "Bentsen",    NULL, "mette.bentsen@mpi-bn.mpg.de",      "ctb"),

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
+export(add_genome_matches)
 export(add_inverse_strand)
 export(add_seq)
+export(add_target_matches)
 export(bed_to_granges)
 export(char_to_granges)
 export(double_flank)

R/06_find_spacers.R

@@ -189,8 +189,8 @@ extract_matchranges <- function(gr, bsgenome, pattern, plot = FALSE){
 #' @param spacer     string: spacer pattern in extended IUPAC alphabet
 #' @param pam        string: pam pattern in extended IUPAC alphabet
 #' @param complement TRUE (default) or FALSE: also search in compl ranges?
-#' @param ontargetmethod  'Doench2016' or 'Doench2016': on-target scoring method
-#' @param offtargetmethod 'bowtie' (default) or 'pdict'
+#' @param ontargetmethod  'Doench2016','Doench2016' or NULL (no on-target score)
+#' @param offtargetmethod 'bowtie', 'pdict', or NULL (no offtarget analysis)
 #' @param offtargetfilterby filter for best off-target counts by this variable
 #' @param subtract_targets TRUE or FALSE (default): whether to subtract target 
 #'                   (mis)matches from offtarget counts

R/07_count_offtargets.R

@@ -507,6 +507,23 @@ count_spacer_matches <- function(
 #==============================================================================
 
 
+#' Add target matches
+#' @param spacers     GRanges
+#' @param targets     GRanges
+#' @param bsgenome    BSgenome
+#' @param mismatches  number
+#' @param pam         string
+#' @param outdir      bowtie output directory
+#' @param verbose     TRUE (default) or FALSE
+#' @examples 
+#' file <- system.file('extdata/SRF.bed', package='multicrispr')
+#' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
+#' targets0 <- bed_to_granges(file, 'mm10')
+#' targets <- extend(targets0)
+#' spacers <- find_spacers(targets, bsgenome, complement = FALSE, 
+#'                         ontargetmethod = NULL, offtargetmethod = NULL)
+#' spacers %<>% add_target_matches(targets, bsgenome)
+#' @export
 add_target_matches <- function(
     spacers, targets, bsgenome, mismatches = 2, pam = 'NGG', 
     outdir = OUTDIR, verbose = TRUE
@@ -542,6 +559,25 @@ add_target_matches <- function(
     
 }
 
+#' Add genome matches
+#' @param spacers            GRanges
+#' @param bsgenome           BSgenome
+#' @param mismatches         number
+#' @param pam                string
+#' @param offtargetmethod    'bowtie' or 'pdict'
+#' @param outdir             bowtie output directory
+#' @param indexedgenomesdir  directory with indexed genomes
+#' @param verbose            TRUE (default) or FALSE
+#' @examples 
+#' file <- system.file('extdata/SRF.bed', package='multicrispr')
+#' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
+#' targets0 <- bed_to_granges(file, 'mm10')
+#' targets <- extend(targets0)
+#' spacers <- find_spacers(targets, bsgenome, complement = FALSE, 
+#'                         ontargetmethod = NULL, offtargetmethod = NULL)
+#' spacers %<>% extract(1:100)
+#' spacers %<>% add_genome_matches(bsgenome)
+#' @export
 add_genome_matches <- function(
     spacers, 
     bsgenome          = getBSgenome(genome(spacers)[1]),
@@ -745,6 +781,7 @@ count_offtargets <- function(spacers, bsgenome, targets = NULL, mismatches = 2,
     indexedgenomesdir = INDEXEDGENOMESDIR, verbose = TRUE, plot = TRUE, ...
 ){
 # First clear
+    if (is.null(offtargetmethod)) return(spacers)
     if (!has_been_indexed(bsgenome, indexedgenomesdir)) return(spacers)
     if (mismatches==-1) return(spacers)
     offcols <- c(paste0('G', 0:3), paste0('T', 0:3), paste0('off', 0:3), 'off')

R/08_score_ontargets.R

@@ -197,6 +197,7 @@ score_ontargets <- function(
     # Assert
     crisprcontext <- NULL
     assert_is_all_of(spacers, 'GRanges')
+    if (is.null(ontargetmethod))  return(spacers)
     assert_is_a_string(ontargetmethod)
     assert_is_subset(ontargetmethod, c('Doench2014', 'Doench2016'))
     if (ontargetmethod %in% names(mcols(spacers))){

man/add_genome_matches.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/07_count_offtargets.R
+\name{add_genome_matches}
+\alias{add_genome_matches}
+\title{Add genome matches}
+\usage{
+add_genome_matches(
+  spacers,
+  bsgenome = getBSgenome(genome(spacers)[1]),
+  mismatches = 2,
+  pam = "NGG",
+  offtargetmethod = c("bowtie", "pdict")[1],
+  outdir = OUTDIR,
+  indexedgenomesdir = INDEXEDGENOMESDIR,
+  verbose = TRUE
+)
+}
+\arguments{
+\item{spacers}{GRanges}
+
+\item{bsgenome}{BSgenome}
+
+\item{mismatches}{number}
+
+\item{pam}{string}
+
+\item{offtargetmethod}{'bowtie' or 'pdict'}
+
+\item{outdir}{bowtie output directory}
+
+\item{indexedgenomesdir}{directory with indexed genomes}
+
+\item{verbose}{TRUE (default) or FALSE}
+}
+\description{
+Add genome matches
+}
+\examples{
+file <- system.file('extdata/SRF.bed', package='multicrispr')
+bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
+targets0 <- bed_to_granges(file, 'mm10')
+targets <- extend(targets0)
+spacers <- find_spacers(targets, bsgenome, complement = FALSE, 
+                        ontargetmethod = NULL, offtargetmethod = NULL)
+spacers \%<>\% extract(1:100)
+spacers \%<>\% add_genome_matches(bsgenome)
+}

man/add_target_matches.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/07_count_offtargets.R
+\name{add_target_matches}
+\alias{add_target_matches}
+\title{Add target matches}
+\usage{
+add_target_matches(
+  spacers,
+  targets,
+  bsgenome,
+  mismatches = 2,
+  pam = "NGG",
+  outdir = OUTDIR,
+  verbose = TRUE
+)
+}
+\arguments{
+\item{spacers}{GRanges}
+
+\item{targets}{GRanges}
+
+\item{bsgenome}{BSgenome}
+
+\item{mismatches}{number}
+
+\item{pam}{string}
+
+\item{outdir}{bowtie output directory}
+
+\item{verbose}{TRUE (default) or FALSE}
+}
+\description{
+Add target matches
+}
+\examples{
+file <- system.file('extdata/SRF.bed', package='multicrispr')
+bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
+targets0 <- bed_to_granges(file, 'mm10')
+targets <- extend(targets0)
+spacers <- find_spacers(targets, bsgenome, complement = FALSE, 
+                        ontargetmethod = NULL, offtargetmethod = NULL)
+spacers \%<>\% add_target_matches(targets, bsgenome)
+}

man/find_spacers.Rd

@@ -33,9 +33,9 @@ find_spacers(
 
 \item{complement}{TRUE (default) or FALSE: also search in compl ranges?}
 
-\item{ontargetmethod}{'Doench2016' or 'Doench2016': on-target scoring method}
+\item{ontargetmethod}{'Doench2016','Doench2016' or NULL (no on-target score)}
 
-\item{offtargetmethod}{'bowtie' (default) or 'pdict'}
+\item{offtargetmethod}{'bowtie', 'pdict', or NULL (no offtarget analysis)}
 
 \item{offtargetfilterby}{filter for best off-target counts by this variable}