TsIOList-class {TAPseq} | R Documentation

## TsIOList class

### Description

TsIOList class is a container to store multiple `TsIO` objects. This enables storing of Primer3 input and output for multiple target genes.

### Usage

    TsIOList(...)

    ## S4 method for signature 'TsIOList'
    sequence_id(x)

    ## S4 method for signature 'TsIOList'
    target_sequence(x)

    ## S4 method for signature 'TsIOList'
    sequence_template(x)

    ## S4 method for signature 'TsIOList'
    target_annot(x)

    ## S4 method for signature 'TsIOList'
    tapseq_primers(x)

    ## S4 method for signature 'TsIOList'
    pcr_products(x)

### Arguments

`...` | Multiple TsIO objects from which a TsIOList object should be created.
`x` | A `TsIOList` object.

### Value

A `TsIOList` object.

### Methods (by generic)

- `sequence_id`: Get sequence_id

- `target_sequence`: Get target_sequence

- `sequence_template`: Create sequence_template

- `target_annot`: Get target_annot

- `tapseq_primers`: Get tapseq_primers

- `pcr_products`: Get pcr_products

### See Also

TsIO

### Examples

    # get example transcript sequences
    data("chr11_truncated_txs_seq")
    txs_seqs <- chr11_truncated_txs_seq[1:2]
    txs_ids <- names(txs_seqs)

    # 10x beads-oligo-dt sequence
    beads_oligo <- "CTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"

    # reverse primer used in all PCR reactions
    reverse_primer <- "CTACACGACGCTCTTCCGATCT"

    # create TsIO objects
    tsio1 <- TsIO(sequence_id = txs_ids[1], target_sequence = txs_seqs[[1]],
                  beads_oligo = beads_oligo, reverse_primer = reverse_primer,
                  product_size_range = c(350, 500))

    tsio2 <- TsIO(sequence_id = txs_ids[2], target_sequence = txs_seqs[[2]],
                  beads_oligo = beads_oligo, reverse_primer = reverse_primer,
                  product_size_range = c(350, 500))

    # create TsIOList object
    obj <- TsIOList(tsio1 = tsio1, tsio2 = tsio2)

    # it's noteworthy to mention that when creating a TsIOList from a DNAStringSet of target
    # sequences, it's easier to use TAPseqInput()
    ?TAPseqInput

    # as with TsIO objects, some values can be accessed using accessor functions
    sequence_template(obj)

[Package TAPseq version 0.99.6 Index]