example-datasets: Example datasets

In sofpn/rprimer: Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Example datasets

Description

The purpose of these datasets is to illustrate the functionality of rprimer. The following datasets are provided:

• exampleRprimerAlignment - a Biostrings::DNAMultipleAlignment object (Pages et al., 2020) containing an alignment of 50 hepatitis E virus sequences collected from NCBI GenBank. See "documentation_example_alignment.txt" within the inst/script folder of this package for more details.

• exampleRprimerProfile - an RprimerProfile object, generated from the alignment above.

• exampleRprimerOligo - an RprimerOligo object, generated from the consensus profile above.

• exampleRprimerAssay - an RprimerAssay object, generated from the oligos above.

• exampleRprimerMatchOligo - an RprimerMatchOligo object, describing how well some oligos match with the sequences in exampleRprimerAlignment.

• exampleRprimerMatchAssay - an RprimerMatchAssay object, describing how well some assays match with the seuqences in exampleRprimerAlignment.

Usage

data("exampleRprimerAlignment")

data("exampleRprimerProfile")

data("exampleRprimerOligo")

data("exampleRprimerAssay")

data("exampleRprimerMatchOligo")

data("exampleRprimerMatchAssay")

Format

An object of class DNAMultipleAlignment with 50 rows and 7597 columns.

An object of class RprimerProfile with 7597 rows and 12 columns.

An object of class RprimerOligo with 322 rows and 26 columns.

An object of class RprimerAssay with 4883 rows and 65 columns.

An object of class RprimerMatchOligo with 10 rows and 13 columns.

An object of class RprimerMatchAssay with 5 rows and 39 columns.

References

H. Pages, P. Aboyoun, R. Gentleman and S. DebRoy (2020). Biostrings: Efficient manipulation of biological strings. R package version 2.57.2.

sofpn/rprimer documentation built on Aug. 19, 2024, 4:19 p.m.