TsIOList-class {TAPseq} | R Documentation |
TsIOList class is a container to store multiple TsIO
objects.
This enables storing of Primer3 input and output for multiple target genes.
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)
... |
Multiple TsIO objects from which a TsIOList object should be created. |
x |
A |
A TsIOList
object.
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
# 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)