R/process_oligo.R
In knoplab/castR: Design and Analysis of Pooled Genome-Wide Libraries
# FUNCTIONS FOR OLIGO PROCESSING ===============================================
#' Landing Sequence Adjustment Table
#'
#' This \code{data.frame} is used to infer the length of landing sequence homology
#' provided in dependence of the absulte cleavage distance from the intended site
#' of integration/feature manipulation for CASTLING.
#' @param hom.in Homology towards the feature site, e. g. 5\' landing sequence
#' for C-terminal tagging.
#' @param hom.ex Homology away from the feature site, e. g. 3\' landing sequence
#' for C-terminal tagging.
#' @param ID Positional argument (not used).
#' @export
LANDING_SEQUENCE_ADJUSTMENT <- data.frame(
# homology lengths towards the ORF
hom.in = c(40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
39, 38, 37, 36, 35, 34, 33, 32, 31,
rep(30, 27)),
# homology lengths outwards the ORF
hom.ex = c(40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27,
27, 27, 27, 27, 27, 27, 27, 27, 27,
seq(27, 1)),
# absolute amount of cleavage distance
ID = seq(0, 49)
)
#' Generate Oligo Pool Sequences for CASTLING
#'
#' This function will expand a (processed) CASTLING lookup table which contains
#' CRISPR target sequences with the respective oligo pool sequences that must be
#' ordered according to the oligo template schemed.
#' @details The CASTLING lookup table must contain at least the \code{ls_5_full},
#' the \code{ls_3_full}, and the \code{target_sequence} sequences, as well as the
#' inferred (signed/directional) \code{cleavage_distance} from the landing
#' sequence junction.
#' @param subject A processed CASTLING lookup table (\code{data.table} object);
#' see details.
#' @param template A string template of the oligonucleotide, in which “\code{str_C}”
#' is replaced by the CRISPR spacer, “\code{str_3}” by the adjusted 3\' landing
#' sequence, and “\code{str_5}” by the adjusted 5\' landing sequence. Landing
#' sequence adjustment is defined in \code{LANDING_SEQUENCE_ADJUSTMENT}.
#' The \code{str_X} parameters can be used to force the reverse complement
#' of the respective element.
#' @param avoid_pattern A character vector of any pattern to avoid during oligo
#' pool design. This can contain IUPAC ambiguity letters from base 3 onwards.
#' @return A \code{data.table} compatible with CASTLING. All sequences are
#' returned in sense orientation.
#' @import data.table
#' @importFrom stringr str_replace
#' @importFrom Biostrings DNAString reverseComplement PDict vcountPDict
#' @export
#' @examples
#' generate_oligo_sequence(my_processed_lookup_table,
#' "aaastr_Ctttstr_5gagcgggcstr_3cggc",
#' avoid_pattern = c("GATATC", "AAGCTT"))
generate_oligo_sequence <- function(subject, template, str_C.RC = FALSE,
str_5.RC = FALSE, str_3.RC = FALSE,
avoid_pattern = character(0)) {
if (is.null(attr(subject, "feature_site"))) stop(
"could not identify intended site of genomic feature manipulation
that 'subject' was created for, attribute 'feature_site' missing"
)
# LANDING SEQUENCE ADJUSTMENT/TRIMMING ---------------------------------------
if (as.logical(attr(subject, "feature_site"))) {
subject[, ls_5_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.ex[
abs(cleavage_distance) + 1]]
subject[, ls_3_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.in[
abs(cleavage_distance) + 1]]
} else {
subject[, ls_5_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.in[
abs(cleavage_distance) + 1]]
subject[, ls_3_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.ex[
abs(cleavage_distance) + 1]]
}
subject[cleavage_distance < 1, ls_5_seq_homology := substr(
ls_5_full,
start = nchar(ls_5_full) - ls_5_homology + cleavage_distance + 1,
stop = nchar(ls_5_full)
)]
subject[cleavage_distance < 1, ls_3_seq_homology := substr(
ls_3_full,
start = 1,
stop = ls_3_homology
)]
subject[cleavage_distance > 0, ls_5_seq_homology := substr(
ls_5_full,
start = nchar(ls_5_full) - ls_5_homology + 1,
stop = nchar(ls_5_full)
)]
subject[cleavage_distance > 0, ls_3_seq_homology := substr(
ls_3_full,
start = 1,
stop = ls_3_homology + cleavage_distance
)]
# OLIGO SEQUENCE ASSEMBLY ----------------------------------------------------
if (str_C.RC) subject[, target_sequence := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(
subject[, target_sequence])))]
if (str_3.RC) subject[, ls_3_seq_homology := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(
subject[, ls_3_seq_homology])))]
if (str_5.RC) subject[, ls_5_seq_homology := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(
subject[, ls_5_seq_homology])))]
subject[, oligo_sequence := template]
subject[, oligo_sequence := mapply(stringr::str_replace, oligo_sequence,
"str_3", ls_3_seq_homology)]
subject[, oligo_sequence := mapply(stringr::str_replace, oligo_sequence,
"str_5", ls_5_seq_homology)]
subject[, oligo_sequence := mapply(stringr::str_replace, oligo_sequence,
"str_C", target_sequence)]
# remove helper columns
subject[, ls_5_seq_homology := NULL]
subject[, ls_3_seq_homology := NULL]
if (str_C.RC) subject[, target_sequence := as.character(Biostrings::reverseComplement(
Biostrings::DNAStringSet(subject[, target_sequence])))]
# ANNOTATION OF INCOMPATIBILITIES --------------------------------------------
if (length(avoid_pattern) > 0) {
# All sequences are supposed to be 5' to 3', no need to reverse complement.
tmp.avoid_pattern <- Biostrings::vcountPDict(Biostrings::PDict(avoid_pattern,
tb.start = 1, tb.width = 3),
Biostrings::DNAStringSet(subject[, oligo_sequence]),
fixed = FALSE, collapse = 2)
subject[, oligo_penalty := tmp.avoid_pattern]
} else {
subject[, oligo_penalty := 0]
}
}
#' Generate a Reference Genome for post-CASTLING NGS Analysis
#'
#' This function will return a (processed) CASTLING lookup table which contains
#' CRISPR target sequences with the respective reference genome sequences that
#' should be used for Vectorette NGS.
#' @details The CASTLING lookup table must contain at least the \code{ls_5_full},
#' the \code{ls_3_full}, and the \code{target_sequence} sequences, as well as the
#' inferred (signed/directional) \code{cleavage_distance} from the landing
#' sequence junction.
#' @param subject A processed CASTLING lookup table (\code{data.table} object);
#' see details.
#' @param template A string template of the oligos, in which “\code{str_C}”
#' is replaced by the CRISPR spacer, “\code{str_3}” by the adjusted 3\' landing
#' sequence, and “\code{str_5}” by the adjusted 5\' landing sequence. Overlapping
#' sequence material with the \code{tagging_cassette} will be removed.
#' @param tagging_cassette The sequence of the tagging cassette intended to be
#' integrated at the genomic site.
#' @param primer The vectorette initiating primer for NGS. Use the annealing part
#' only.
#' @return A \code{data.table} compatible with CASTLING. All sequences are
#' returned in sense orientation.
#' @import data.table
#' @importFrom utils head tail
#' @importFrom stringr str_locate str_replace
#' @importFrom Biostrings DNAString reverseComplement matchPattern
#' @export
#' @examples
#' my_ref_table <- generate_reference_genome(my_processed_lookup_table,
#' "aaastr_Ctttstr_5gagcgggcstr_3cggc",
#' tagging_cassette = my_cassette,
#' primer = "gtcgacctgcagcgtacg")
#'
#' data.table::fwrite(my_ref_table[, .(oligo_id, junction)], sep = "\n",
#' row.names = FALSE, col.names = FALSE, file = my_file)
generate_reference_genome <- function(subject, template, tagging_cassette,
primer) {
if (is.null(attr(subject, "feature_site"))) stop(
"could not identify intended site of genomic feature manipulation
that 'subject' was created for, attribute 'feature_site' missing"
)
feature_site <- as.logical(attr(subject, "feature_site"))
# IDENTIFICATION OF PRIMER BINDING -------------------------------------------
# cast character vector to DNAString object
dna.prm <- Biostrings::DNAString(primer)
dna.cas <- Biostrings::DNAString(tagging_cassette)
# the 3' LS will be sequenced when:
primer_bind.fwd <- Biostrings::matchPattern(dna.prm,
dna.cas)@ranges
# the 5' LS will be sequenced when:
primer_bind.rev <- Biostrings::matchPattern(reverseComplement(dna.prm),
dna.cas)@ranges
if (!any(primer_bind.rev@start, primer_bind.fwd@start))
stop("primer does not bind in tagging cassette")
# IDENTIFICATION OF TEMPLATE/CASSETTE OVERLAP --------------------------------
find_prefix <- function(str_A, str_B) for (i in 1:nchar(str_A))
if (startsWith(tolower(str_B), substr(tolower(str_A), i, nchar(str_A)))) return(i)
find_suffix <- function(str_A, str_B) for (i in nchar(str_A):1)
if (endsWith(tolower(str_B), substr(tolower(str_A), 1, i))) return(i)
# REPLACEMENT OF TARGET SEQUENCE ---------------------------------------------
replace_str_C <- function(x, str_C.RC = FALSE) {
if (str_C.RC) x[, target_sequence := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(x[, target_sequence])))]
x[, junction := mapply(stringr::str_replace, junction,
"str_C", target_sequence)]
if (str_C.RC) x[, target_sequence := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(x[, target_sequence])))]
x[, oligo_id := paste(oligo_id, target_sequence, sep = "|")]
}
# ASSEMBLY OF REFERENCE GENOME SEQUENCE --------------------------------------
# add information on potential sequence redundancy
sub.subject <- merge(subject, subject[, .N, by = ORF_name.long],
by = "ORF_name.long")
sub.subject[, oligo_id := paste(">lcl", ORF_name.long, sep = "|")]
# The primer binds on forward strand of tagging cassette, the 5' site of the
# template becomes relevant up to the 3' LS.
if (any(primer_bind.fwd@start)) {
seq_from.cas <- substr(tagging_cassette, start = primer_bind.fwd@start,
stop = nchar(tagging_cassette))
seq_from.tmp <- utils::head(unlist(stringr::str_split(template, "str_3")), 1)
# check/correct overlap
tmp.pos <- find_suffix(seq_from.tmp, seq_from.cas)
if (!is.null(tmp.pos)) seq_from.tmp <- substr(seq_from.tmp,
start = tmp.pos + 1, stop = nchar(seq_from.tmp))
sub.subject[, junction := paste0(seq_from.cas, seq_from.tmp, ls_3_full)]
if (grepl("str_C", seq_from.tmp)) {
replace_str_C(sub.subject, feature_site)
} else {
sub.subject <- sub.subject[sub.subject[, .I[which.max(ls_3_homology
+ ifelse(cleavage_distance > 0, cleavage_distance, 0))], by = ORF_name.long]$V1]
}
sub.subject[, oligo_id := paste(oligo_id, nchar(junction) - nchar(ls_3_full)
+ ls_3_homology + ifelse(cleavage_distance > 0,
cleavage_distance, 0) + 1,
nchar(junction), N, sep = "|")]
}
# The primer binds on reverse strand of tagging cassette, the 3' site of the
# template becomes relevant up to the 5' LS.
if (any(primer_bind.rev@start)) {
seq_from.cas <- substr(tagging_cassette, start = 1,
stop = primer_bind.rev@start + primer_bind.rev@width - 1)
seq_from.tmp <- utils::tail(unlist(stringr::str_split(template, "str_5")), 1)
# check/correct overlap
tmp.pos <- find_prefix(seq_from.tmp, seq_from.cas)
if (!is.null(tmp.pos)) seq_from.tmp <- substr(seq_from.tmp,
start = 1, stop = tmp.pos - 1)
sub.subject[, junction := paste0(ls_5_full, seq_from.tmp, seq_from.cas)]
if (grepl("str_C", seq_from.tmp)) {
replace_str_C(sub.subject, feature_site)
} else {
sub.subject <- sub.subject[sub.subject[, .I[which.max(ls_5_homology
- ifelse(cleavage_distance < 0, cleavage_distance, 0))], by = ORF_name.long]$V1]
}
sub.subject[, oligo_id := paste(oligo_id, 1, nchar(ls_5_full)
- ls_5_homology + ifelse(cleavage_distance < 0,
cleavage_distance, 0),
N, sep = "|")]
}
# re-sample
sub.subject <- sub.subject[sample(1:nrow(sub.subject)), ]
return(sub.subject)
}
knoplab/castR documentation built on May 29, 2019, 3:39 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# FUNCTIONS FOR OLIGO PROCESSING ===============================================
#' Landing Sequence Adjustment Table
#'
#' This \code{data.frame} is used to infer the length of landing sequence homology
#' provided in dependence of the absulte cleavage distance from the intended site
#' of integration/feature manipulation for CASTLING.
#' @param hom.in Homology towards the feature site, e. g. 5\' landing sequence
#' for C-terminal tagging.
#' @param hom.ex Homology away from the feature site, e. g. 3\' landing sequence
#' for C-terminal tagging.
#' @param ID Positional argument (not used).
#' @export
LANDING_SEQUENCE_ADJUSTMENT <- data.frame(
# homology lengths towards the ORF
hom.in = c(40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
39, 38, 37, 36, 35, 34, 33, 32, 31,
rep(30, 27)),
# homology lengths outwards the ORF
hom.ex = c(40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27,
27, 27, 27, 27, 27, 27, 27, 27, 27,
seq(27, 1)),
# absolute amount of cleavage distance
ID = seq(0, 49)
)
#' Generate Oligo Pool Sequences for CASTLING
#'
#' This function will expand a (processed) CASTLING lookup table which contains
#' CRISPR target sequences with the respective oligo pool sequences that must be
#' ordered according to the oligo template schemed.
#' @details The CASTLING lookup table must contain at least the \code{ls_5_full},
#' the \code{ls_3_full}, and the \code{target_sequence} sequences, as well as the
#' inferred (signed/directional) \code{cleavage_distance} from the landing
#' sequence junction.
#' @param subject A processed CASTLING lookup table (\code{data.table} object);
#' see details.
#' @param template A string template of the oligonucleotide, in which “\code{str_C}”
#' is replaced by the CRISPR spacer, “\code{str_3}” by the adjusted 3\' landing
#' sequence, and “\code{str_5}” by the adjusted 5\' landing sequence. Landing
#' sequence adjustment is defined in \code{LANDING_SEQUENCE_ADJUSTMENT}.
#' The \code{str_X} parameters can be used to force the reverse complement
#' of the respective element.
#' @param avoid_pattern A character vector of any pattern to avoid during oligo
#' pool design. This can contain IUPAC ambiguity letters from base 3 onwards.
#' @return A \code{data.table} compatible with CASTLING. All sequences are
#' returned in sense orientation.
#' @import data.table
#' @importFrom stringr str_replace
#' @importFrom Biostrings DNAString reverseComplement PDict vcountPDict
#' @export
#' @examples
#' generate_oligo_sequence(my_processed_lookup_table,
#' "aaastr_Ctttstr_5gagcgggcstr_3cggc",
#' avoid_pattern = c("GATATC", "AAGCTT"))
generate_oligo_sequence <- function(subject, template, str_C.RC = FALSE,
str_5.RC = FALSE, str_3.RC = FALSE,
avoid_pattern = character(0)) {
if (is.null(attr(subject, "feature_site"))) stop(
"could not identify intended site of genomic feature manipulation
that 'subject' was created for, attribute 'feature_site' missing"
)
# LANDING SEQUENCE ADJUSTMENT/TRIMMING ---------------------------------------
if (as.logical(attr(subject, "feature_site"))) {
subject[, ls_5_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.ex[
abs(cleavage_distance) + 1]]
subject[, ls_3_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.in[
abs(cleavage_distance) + 1]]
} else {
subject[, ls_5_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.in[
abs(cleavage_distance) + 1]]
subject[, ls_3_homology := LANDING_SEQUENCE_ADJUSTMENT$hom.ex[
abs(cleavage_distance) + 1]]
}
subject[cleavage_distance < 1, ls_5_seq_homology := substr(
ls_5_full,
start = nchar(ls_5_full) - ls_5_homology + cleavage_distance + 1,
stop = nchar(ls_5_full)
)]
subject[cleavage_distance < 1, ls_3_seq_homology := substr(
ls_3_full,
start = 1,
stop = ls_3_homology
)]
subject[cleavage_distance > 0, ls_5_seq_homology := substr(
ls_5_full,
start = nchar(ls_5_full) - ls_5_homology + 1,
stop = nchar(ls_5_full)
)]
subject[cleavage_distance > 0, ls_3_seq_homology := substr(
ls_3_full,
start = 1,
stop = ls_3_homology + cleavage_distance
)]
# OLIGO SEQUENCE ASSEMBLY ----------------------------------------------------
if (str_C.RC) subject[, target_sequence := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(
subject[, target_sequence])))]
if (str_3.RC) subject[, ls_3_seq_homology := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(
subject[, ls_3_seq_homology])))]
if (str_5.RC) subject[, ls_5_seq_homology := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(
subject[, ls_5_seq_homology])))]
subject[, oligo_sequence := template]
subject[, oligo_sequence := mapply(stringr::str_replace, oligo_sequence,
"str_3", ls_3_seq_homology)]
subject[, oligo_sequence := mapply(stringr::str_replace, oligo_sequence,
"str_5", ls_5_seq_homology)]
subject[, oligo_sequence := mapply(stringr::str_replace, oligo_sequence,
"str_C", target_sequence)]
# remove helper columns
subject[, ls_5_seq_homology := NULL]
subject[, ls_3_seq_homology := NULL]
if (str_C.RC) subject[, target_sequence := as.character(Biostrings::reverseComplement(
Biostrings::DNAStringSet(subject[, target_sequence])))]
# ANNOTATION OF INCOMPATIBILITIES --------------------------------------------
if (length(avoid_pattern) > 0) {
# All sequences are supposed to be 5' to 3', no need to reverse complement.
tmp.avoid_pattern <- Biostrings::vcountPDict(Biostrings::PDict(avoid_pattern,
tb.start = 1, tb.width = 3),
Biostrings::DNAStringSet(subject[, oligo_sequence]),
fixed = FALSE, collapse = 2)
subject[, oligo_penalty := tmp.avoid_pattern]
} else {
subject[, oligo_penalty := 0]
}
}
#' Generate a Reference Genome for post-CASTLING NGS Analysis
#'
#' This function will return a (processed) CASTLING lookup table which contains
#' CRISPR target sequences with the respective reference genome sequences that
#' should be used for Vectorette NGS.
#' @details The CASTLING lookup table must contain at least the \code{ls_5_full},
#' the \code{ls_3_full}, and the \code{target_sequence} sequences, as well as the
#' inferred (signed/directional) \code{cleavage_distance} from the landing
#' sequence junction.
#' @param subject A processed CASTLING lookup table (\code{data.table} object);
#' see details.
#' @param template A string template of the oligos, in which “\code{str_C}”
#' is replaced by the CRISPR spacer, “\code{str_3}” by the adjusted 3\' landing
#' sequence, and “\code{str_5}” by the adjusted 5\' landing sequence. Overlapping
#' sequence material with the \code{tagging_cassette} will be removed.
#' @param tagging_cassette The sequence of the tagging cassette intended to be
#' integrated at the genomic site.
#' @param primer The vectorette initiating primer for NGS. Use the annealing part
#' only.
#' @return A \code{data.table} compatible with CASTLING. All sequences are
#' returned in sense orientation.
#' @import data.table
#' @importFrom utils head tail
#' @importFrom stringr str_locate str_replace
#' @importFrom Biostrings DNAString reverseComplement matchPattern
#' @export
#' @examples
#' my_ref_table <- generate_reference_genome(my_processed_lookup_table,
#' "aaastr_Ctttstr_5gagcgggcstr_3cggc",
#' tagging_cassette = my_cassette,
#' primer = "gtcgacctgcagcgtacg")
#'
#' data.table::fwrite(my_ref_table[, .(oligo_id, junction)], sep = "\n",
#' row.names = FALSE, col.names = FALSE, file = my_file)
generate_reference_genome <- function(subject, template, tagging_cassette,
primer) {
if (is.null(attr(subject, "feature_site"))) stop(
"could not identify intended site of genomic feature manipulation
that 'subject' was created for, attribute 'feature_site' missing"
)
feature_site <- as.logical(attr(subject, "feature_site"))
# IDENTIFICATION OF PRIMER BINDING -------------------------------------------
# cast character vector to DNAString object
dna.prm <- Biostrings::DNAString(primer)
dna.cas <- Biostrings::DNAString(tagging_cassette)
# the 3' LS will be sequenced when:
primer_bind.fwd <- Biostrings::matchPattern(dna.prm,
dna.cas)@ranges
# the 5' LS will be sequenced when:
primer_bind.rev <- Biostrings::matchPattern(reverseComplement(dna.prm),
dna.cas)@ranges
if (!any(primer_bind.rev@start, primer_bind.fwd@start))
stop("primer does not bind in tagging cassette")
# IDENTIFICATION OF TEMPLATE/CASSETTE OVERLAP --------------------------------
find_prefix <- function(str_A, str_B) for (i in 1:nchar(str_A))
if (startsWith(tolower(str_B), substr(tolower(str_A), i, nchar(str_A)))) return(i)
find_suffix <- function(str_A, str_B) for (i in nchar(str_A):1)
if (endsWith(tolower(str_B), substr(tolower(str_A), 1, i))) return(i)
# REPLACEMENT OF TARGET SEQUENCE ---------------------------------------------
replace_str_C <- function(x, str_C.RC = FALSE) {
if (str_C.RC) x[, target_sequence := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(x[, target_sequence])))]
x[, junction := mapply(stringr::str_replace, junction,
"str_C", target_sequence)]
if (str_C.RC) x[, target_sequence := as.character(
Biostrings::reverseComplement(Biostrings::DNAStringSet(x[, target_sequence])))]
x[, oligo_id := paste(oligo_id, target_sequence, sep = "|")]
}
# ASSEMBLY OF REFERENCE GENOME SEQUENCE --------------------------------------
# add information on potential sequence redundancy
sub.subject <- merge(subject, subject[, .N, by = ORF_name.long],
by = "ORF_name.long")
sub.subject[, oligo_id := paste(">lcl", ORF_name.long, sep = "|")]
# The primer binds on forward strand of tagging cassette, the 5' site of the
# template becomes relevant up to the 3' LS.
if (any(primer_bind.fwd@start)) {
seq_from.cas <- substr(tagging_cassette, start = primer_bind.fwd@start,
stop = nchar(tagging_cassette))
seq_from.tmp <- utils::head(unlist(stringr::str_split(template, "str_3")), 1)
# check/correct overlap
tmp.pos <- find_suffix(seq_from.tmp, seq_from.cas)
if (!is.null(tmp.pos)) seq_from.tmp <- substr(seq_from.tmp,
start = tmp.pos + 1, stop = nchar(seq_from.tmp))
sub.subject[, junction := paste0(seq_from.cas, seq_from.tmp, ls_3_full)]
if (grepl("str_C", seq_from.tmp)) {
replace_str_C(sub.subject, feature_site)
} else {
sub.subject <- sub.subject[sub.subject[, .I[which.max(ls_3_homology
+ ifelse(cleavage_distance > 0, cleavage_distance, 0))], by = ORF_name.long]$V1]
}
sub.subject[, oligo_id := paste(oligo_id, nchar(junction) - nchar(ls_3_full)
+ ls_3_homology + ifelse(cleavage_distance > 0,
cleavage_distance, 0) + 1,
nchar(junction), N, sep = "|")]
}
# The primer binds on reverse strand of tagging cassette, the 3' site of the
# template becomes relevant up to the 5' LS.
if (any(primer_bind.rev@start)) {
seq_from.cas <- substr(tagging_cassette, start = 1,
stop = primer_bind.rev@start + primer_bind.rev@width - 1)
seq_from.tmp <- utils::tail(unlist(stringr::str_split(template, "str_5")), 1)
# check/correct overlap
tmp.pos <- find_prefix(seq_from.tmp, seq_from.cas)
if (!is.null(tmp.pos)) seq_from.tmp <- substr(seq_from.tmp,
start = 1, stop = tmp.pos - 1)
sub.subject[, junction := paste0(ls_5_full, seq_from.tmp, seq_from.cas)]
if (grepl("str_C", seq_from.tmp)) {
replace_str_C(sub.subject, feature_site)
} else {
sub.subject <- sub.subject[sub.subject[, .I[which.max(ls_5_homology
- ifelse(cleavage_distance < 0, cleavage_distance, 0))], by = ORF_name.long]$V1]
}
sub.subject[, oligo_id := paste(oligo_id, 1, nchar(ls_5_full)
- ls_5_homology + ifelse(cleavage_distance < 0,
cleavage_distance, 0),
N, sep = "|")]
}
# re-sample
sub.subject <- sub.subject[sample(1:nrow(sub.subject)), ]
return(sub.subject)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.