TsIOList-class: TsIOList class

In argschwind/TAPseq: Targeted scRNA-seq primer design for TAP-seq

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(TsIOList): Get sequence_id

• target_sequence(TsIOList): Get target_sequence

• sequence_template(TsIOList): Create sequence_template

• target_annot(TsIOList): Get target_annot

• tapseq_primers(TsIOList): Get tapseq_primers

• pcr_products(TsIOList): 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)

argschwind/TAPseq documentation built on Feb. 9, 2024, 8:20 p.m.