TsIO-class {TAPseq} | R Documentation |
TsIO objects store TAP-seq Primer3 input and output.
TsIO( sequence_id, target_sequence, beads_oligo, reverse_primer, product_size_range, target_annot = NULL, primer_num_return = 5, min_primer_region = 100, primer_opt_tm = NA, primer_min_tm = NA, primer_max_tm = NA ) ## S4 method for signature 'TsIO' sequence_id(x) ## S4 replacement method for signature 'TsIO' sequence_id(x) <- value ## S4 method for signature 'TsIO' target_sequence(x) ## S4 replacement method for signature 'TsIO' target_sequence(x) <- value ## S4 method for signature 'TsIO' beads_oligo(x) ## S4 replacement method for signature 'TsIO' beads_oligo(x) <- value ## S4 method for signature 'TsIO' reverse_primer(x) ## S4 replacement method for signature 'TsIO' reverse_primer(x) <- value ## S4 method for signature 'TsIO' target_annot(x) ## S4 replacement method for signature 'TsIO' target_annot(x) <- value ## S4 method for signature 'TsIO' product_size_range(x) ## S4 replacement method for signature 'TsIO' product_size_range(x) <- value ## S4 method for signature 'TsIO' primer_num_return(x) ## S4 replacement method for signature 'TsIO' primer_num_return(x) <- value ## S4 method for signature 'TsIO' min_primer_region(x) ## S4 replacement method for signature 'TsIO' min_primer_region(x) <- value ## S4 method for signature 'TsIO' primer_opt_tm(x) ## S4 replacement method for signature 'TsIO' primer_opt_tm(x) <- value ## S4 method for signature 'TsIO' primer_min_tm(x) ## S4 replacement method for signature 'TsIO' primer_min_tm(x) <- value ## S4 method for signature 'TsIO' primer_max_tm(x) ## S4 replacement method for signature 'TsIO' primer_max_tm(x) <- value ## S4 method for signature 'TsIO' sequence_template(x) ## S4 method for signature 'TsIO' tapseq_primers(x) ## S4 method for signature 'TsIO' pcr_products(x)
sequence_id |
Name ( |
target_sequence |
A |
beads_oligo |
Beads-oligo-dT sequence for the used droplet sequencing protocol (10x, Drop-seq). |
reverse_primer |
Reverse primer sequence used for all PCR reactions. |
product_size_range |
Numerical vector of length 2 specifying the desired length of the resulting amplicons. |
target_annot |
(optional) A |
primer_num_return |
How many forward primers should be designed? (default: 5) |
min_primer_region |
Minimum sequence length required for primer design. Mostly relevant in
case the sequence template is too short to allow the specified |
primer_opt_tm, primer_min_tm, primer_max_tm |
Optimal, minumum and maximum primer melting temperature. |
x |
A |
value |
A valid value to assign to the chosen slot. |
tapseq_primers |
Slot where designed TAP-seq primers are stored. Not set by user. |
pcr_products |
Slot where PCR products of primers are stored. Not set by user. |
The TsIO class is based on the Boulder IO records used by Primer3 (Primer3 manual). These objects are used to store the sequence templates and parameters needed for TAP-seq primer design. Primers designed with Primer3 are also stored in the same TsIO objects.
Use TsIO()
to construct a new TsIO object from scratch.
A TsIO
object.
sequence_id
: Get sequence_id
sequence_id<-
: Set sequence_id
target_sequence
: Get target_sequence
target_sequence<-
: Set target_sequence
beads_oligo
: Get beads_oligo
beads_oligo<-
: Set beads_oligo
reverse_primer
: Get reverse_primer
reverse_primer<-
: Set reverse_primer
target_annot
: Get target_annot
target_annot<-
: Set target_annot
product_size_range
: Get product_size_range
product_size_range<-
: Set product_size_range
primer_num_return
: Get primer_num_return
primer_num_return<-
: Set primer_num_return
min_primer_region
: Get min_primer_region
min_primer_region<-
: Set min_primer_region
primer_opt_tm
: Get primer_opt_tm
primer_opt_tm<-
: Set primer_opt_tm
primer_min_tm
: Get primer_min_tm
primer_min_tm<-
: Set primer_min_tm
primer_max_tm
: Get primer_max_tm
primer_max_tm<-
: Set primer_max_tm
sequence_template
: Create sequence_template
tapseq_primers
: Get tapseq_primers
pcr_products
: Get pcr_products
http://primer3.org/manual.html for Primer3 manual.
# get example transcript sequence data("chr11_truncated_txs_seq") tx_seq <- chr11_truncated_txs_seq[[1]] tx_id <- names(chr11_truncated_txs_seq)[1] # 10x beads-oligo-dt sequence beads_oligo <- "CTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" # reverse primer used in all PCR reactions reverse_primer <- "CTACACGACGCTCTTCCGATCT" # create TsIO object obj <- TsIO(sequence_id = tx_id, target_sequence = tx_seq, beads_oligo = beads_oligo, reverse_primer = reverse_primer, product_size_range = c(350, 500)) # slot values can be accessed using accessor functions sequence_id(obj) sequence_id(obj) <- "Gene1" sequence_id(obj) # the sequence template (target sequence + reverse complement of beads-oligo-dt) for primer # design can be viewed as well sequence_template(obj)