Data: Data Sets.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Data Sets.

Description

Ippolito

IGHV primer data from Ippolito et al.

Tiller

IGHV primer data from Tiller et al.

Comparison

Evaluated primer sets targeting the functional human IGH immunoglobulin genes. The sets were generated using the default evaluation settings of openPrimeR. The primer sets were gathered from IMGT and the literature.

RefCoverage

Experimental results of multiplex PCR.

Usage

data(Comparison)

data(Ippolito)

data(RefCoverage)

data(Tiller)

Format

For the RefCoverage data set, the feature.matrix data frame contains the properties of the primer set from Tiller et al. as well as a primer set that was designed by openPrimeR. The column Experimental_Coverage indicates the experimentally determined coverage, while the other columns relate to properties of the primers that were computed with openPrimeR. The ref.data list contains the raw experimental coverage of individual primers from the primer sets from Tiller and openPrimeR, which both target templates from the IGH locus. The rows of the data frames indicate primers and the columns indicate IGH templates for which experimental coverage was determined. The cell entries are hex codes. Each hex code represents a color indicating a certain experimental coverage status. Hex codes representing red shades indicate no or little amplification, while hex codes for green shades indicate high yields.

For the Ippolito data set, primer.df provides a Primers object containing the evaluated set of primers from Tiller et al. template.df provides a Templates object containing functional, human IGHV templates for, and settings provides a DesignSettings object providing the used analysis settings.

For the Comparison data set, primer.data and template.data are lists of Primers and Templates objects, respectively.

For the Tiller data set, tiller.primer.df provides a Primers object, tiller.template.df provides the corresponding Templates object, and tiller.settings provides the DesignSettings object that was used for evaluating tiller.primer.df.

References

IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France).

Ippolito GC, Hoi KH, Reddy ST, Carroll SM, Ge X, Rogosch T, Zemlin M, Shultz LD, Ellington AD, VanDenBerg CL, Georgiou G. 2012. Antibody Repertoires in Humanized NOD-scid-IL2R gamma null Mice and Human B Cells Reveals Human-Like Diversification and Tolerance Checkpoints in the Mouse. PLoS One 7:e35497.

Tiller, Thomas, et al. "Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning." Journal of immunological methods 329.1 (2008): 112-124.

Examples

# Load the comparison data
data(Comparison)
# Explore the first entry of the primer and template data:
primer.data[[1]]
template.data[[1]]
# Summarize the primer properties:
get_comparison_table(template.data, primer.data)

# Load the data from Ippolito et al.
data(Ippolito)
primer.df
template.df
constraints(settings)

# Load experimental PCR results
data(RefCoverage)

# Load the data from Tiller et al.
data(Tiller)
tiller.primer.df
tiller.template.df
constraints(tiller.settings)

matdoering/openPrimeR documentation built on Feb. 11, 2024, 9:22 p.m.