accessors: Accessors for TsIO objects

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

Accessors for TsIO objects

Description

A set of functions for getting/setting/modifying the data stored in TsIO or TsIOList class objects.

Usage

sequence_id(x)

sequence_id(x) <- value

target_sequence(x)

target_sequence(x) <- value

beads_oligo(x)

beads_oligo(x) <- value

reverse_primer(x)

reverse_primer(x) <- value

target_annot(x)

target_annot(x) <- value

product_size_range(x)

product_size_range(x) <- value

primer_num_return(x)

primer_num_return(x) <- value

min_primer_region(x)

min_primer_region(x) <- value

primer_opt_tm(x)

primer_opt_tm(x) <- value

primer_min_tm(x)

primer_min_tm(x) <- value

primer_max_tm(x)

primer_max_tm(x) <- value

sequence_template(x)

tapseq_primers(x)

pcr_products(x)

Arguments

x	A TsIO or TsIOList class object.
value	A valid value to assign to the chosen slot.

Value

Returns the stored value(s) of a slot, or sets a new value

Examples

# chr11 primers example data
data("chr11_primers")

# slot values of TsIO objects can be accessed using accessor functions
tsio <- chr11_primers[[1]]
sequence_id(tsio)
sequence_id(tsio) <- "Gene1"
sequence_id(tsio)

# some slots can only be obtained, but not set as filling these is part of the TAPseq workflow
tapseq_primers(tsio)
pcr_products(tsio)

# sequence templates can be created
sequence_template(tsio)

# values of TsIOList object slots can be extracted as well, but not set
tsio_list <- chr11_primers[1:2]
sequence_id(tsio_list)
target_sequence(tsio_list)
target_annot(tsio_list)
tapseq_primers(tsio_list)
pcr_products(tsio_list)
sequence_template(tsio_list)

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