TsIO-class {TAPseq} | R Documentation

## TsIO class

### Description

TsIO objects store TAP-seq Primer3 input and output.

### Usage

    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)

### Arguments

`sequence_id` | Name (`character`) of the target sequence, e.g. the gene name. It's adviced to use meaningful sequence ids to savely assign designed primers to their targets.
`target_sequence` | A `DNAString` or `character` object containing the target sequence for which primers should be designed. Usually a transcript sequence.
`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 `GRanges` object with transcript annotation in case the target is a transcript of a gene locus. If provided, it should contain all exons of the targeted transcript.
`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 `product_size_range`.
`primer_opt_tm, primer_min_tm, primer_max_tm` | Optimal, minumum and maximum primer melting temperature.
`x` | A `TsIO` object.
`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.

### Details

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.

### Value

A `TsIO` object.

### Methods (by generic)

- `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

### See Also

http://primer3.org/manual.html for Primer3 manual.

### Examples

    # 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)

[Package TAPseq version 0.99.6 Index]