Man pages for matdoering/openPrimeR
Multiplex PCR Primer Design and Analysis
| AbstractConstraintSettings-class | AbstractClass for Constraint Settings. |
| add.coverage.constraints | Addition of Coverage Constraints. |
| add.dimerization.constraints | Addition of Dimerization Constraints |
| add.uniform.leaders.to.seqs | Add Uniform Binding Regions. |
| adjust.ORF.start | Adjust ORF position |
| align.seqs | Multiple Sequence Alignment |
| align.structures | Formatting of Dimerization Structures. |
| AnalysisStats | Primer Analysis Statistics. |
| ancestor_of | Tree Ancestry |
| annealing.temp.rule.of.thumb | Rule of thumb for annealing temperature |
| annotate.binding.events | Annotation of Primer Binding Events. |
| apply.constraint | Application of Constraints |
| apply.constraint.list | Apply Constraints to a List. |
| assign_binding_regions.character | Character Assignment of Binding Regions |
| assign_binding_regions.numeric | Numeric Assignment of Binding Regions. |
| augment.primer.cvg | Augmentation of Primer Coverage. |
| batchify | Creates multiple Batches for Parallelization. |
| batchify.simple | Simple Batchification |
| batchify.temp | Batchification by Temperature. |
| build.gain.df | Gain of Coverage by Excluded Primers. |
| build.ILP.df | Construction of ILP Results. |
| build_leader_df | Building of Leader Data Frame. |
| build.tool.overview | Creation of an Overview of Third-Party Tools. |
| call.melt | Thermodynamic melting temperature computations. |
| call.melt.single | Thermodynamic melting temperature computations. |
| cascaded.filter | Filtering for the Optimization |
| cascaded.filter.quick | Cascaded Filter |
| cbind.Primers | cbind for Primers class. |
| cbind.Templates | cbind for Template class. |
| check.3prime.hexamers | 3' Hexamer Check. |
| check.3prime.mismatches | 3' Mismatch Check. |
| check_constraints_comparison | Batch Procedure for Evaluating Primer Sets. |
| check_constraint_settings_validity | Check the Validity of the Constraint Settings. |
| check_correspondence | Check of Primer and Template Correspondence. |
| check_cvg_constraints | Evaluation of Coverage Constraints. |
| check.init.primer.length | Primer Length Check. |
| check.init.primer.length.single | Primer Length Check. |
| check_interval | Check Constraint Intervals |
| check_limits | Validity Check for Limits. |
| check_limit_value | Check of limit correctness. |
| check.mutations | Identification of Mismatch Mutations. |
| check_names | Check Setting Names. |
| check_report_deps | Check for Report Dependencies. |
| check_restriction_sites_single | Identification of Sequence Restriction Sites. |
| check_setting | Check Setting Validity. |
| check_settings_validity | Validity Check for DesignSettings. |
| check.template.constraints | Check Constraints on Templates |
| check.tool.function | Check Functionality of Third-Party Tools. |
| check.tool.installation | Check Tool Installation |
| combine.binding.events | Combination of Binding Events. |
| combine.strings | Combination of OligoArrayAux Structure Sequences. |
| comp | Sequence complement |
| compare.constraints | Constraint list comparison |
| comparison.cvg | Comparison Coverage Stats. |
| comparison.stats.raw | Computation of Raw Stats for Primer Comparison |
| complement.sequence | Sequence complement |
| compute.all.cross.dimers | Cross dimerization |
| compute.all.cross.dimers.frontend | Cross Dimerization. |
| compute.all.cross.dimers.unfiltered | Cross dimerization |
| compute.all.primer.subsets.ILP | Computation of Primer Subsets |
| compute.all.self.dimers | Self dimers |
| compute.all.self.dimers.frontend | Self Dimerization. |
| compute_annealing_temp | Annealing temperature. |
| compute.basic.details | Computation of Coverage Details |
| compute.constraints | Computation of Constraints. |
| compute.covered.Ta | Annealing temperature |
| compute.dimer.matrix | Dimerization matrix |
| compute.efficiency | Primer Efficiency. |
| compute.empiric.melting.temp | Non-Thermodynamic Computation of Melting Temperatures. |
| compute.gc.ratio | GC ratio |
| compute.melting.temps | Computation of Melting Temperatures. |
| compute.melting.temps.thermo | Computation of Thermodynamic Melting Temperatures. |
| compute.mismatch.table | Mismatch overview table |
| compute.primer.efficiencies | Primer Efficiency. |
| compute.secondary.structures | Secondary Structure Computations. |
| compute.sodium.equivalent.conc | Sodium-equivalent Concentration |
| compute.structure.vienna | Computation of Secondary Structures with ViennaRNA. |
| compute.Ta | Annealing temperature |
| compute.template.secondary.structures | Template Secondary Structures |
| compute.Tm.baldino | Baldino Formula |
| compute.Tm.sets | Cross-Dimerization Filtering |
| compute.unique.covered.idx | Unique Coverage Indices Computes the indices of templates... |
| condition | Condition Constructor |
| consecutive.GC.count | Consecutive GCs |
| con_select | Quick Selection of Constraints. |
| constraints.to.df | Conversion of Constraints List to Data Frame. |
| constraints_to_unit | Mapping of Constraints to Units. |
| constraints.xml.format | Constraint XML Format. |
| convert.from.iupac | Conversion from IUPAC nucleotides |
| convert.PCR.units | Conversion of PCR Units |
| convert.temperature | Conversion between Celsius and Kelvin |
| convert.to.iupac | Merge sequences. |
| copy.melt.config | Copy MELTING Config File |
| covered.primers.to.ID.string | Conversion of Primer Indices to ID string |
| covered.seqs.to.ID.string | Conversion of Template Coverage Indices to ID string |
| covered.seqs.to.idx | Conversion of Coverage Strings to Indices. |
| create.constraint.table | Output a Constraint Overview Table |
| create.constraint.XML | XML Output of Constraints |
| create.cvg.text | Coverage Info Text |
| create_fulfilled_counts | Creation of Fulfilled/Failed Constraint Counts. |
| create.G.matrix | Create free energy matrix |
| create.initial.primer.set | Creation of an Initial Primer Set. |
| create.kmer | Creation of k-mers of a single sequence. |
| create.k.mers | Creation of k-mers for multiple sequences. |
| create.options.table | Creation of a Table for Constraint Options. |
| create.other.table | Creation of a Table for Other Constraint Settings. |
| create.PCR.table | Creation of a Table for PCR Conditions |
| create.primer.ranges | Ranges for Initial Primers. |
| create.primers.naive | Naive Initialization of Primers. |
| create.primers.tree | Tree-based Initialization of Primers. |
| create_report-list-list-method | Creation of a PDF Report for Primer Comparison. |
| create_report-Primers-Templates-method | Creation of a PDF report. |
| create.Tm.brackets | Creation of Melting Temperature Groups |
| create.uniform.leaders | Uniform Binding Ranges. |
| Data | Data Sets. |
| design_primers.single | Design Primers for a Single Direction |
| detect.gap.columns | Identification of Gappy Columns in Alignments. |
| dimerization.table | Dimerization Table. |
| dir.copy | Copy Directories. |
| disambiguate.primers | Disambiguation of Primers. |
| estimate.cvg | Estimation of Primer Coverage. |
| estimate.cvg.dir | Estimation of Primer Coverage. |
| eval.comparison.primers | Evaluation of Primers for Comparison |
| eval.constraints | Evaluation of Constraints' |
| evaluate.basic.cvg | Evaluation of Primer Coverage. |
| evaluate.constrained.cvg | Evaluation of Primer Coverage. |
| evaluate.cvg | Evaluation of Coverage. |
| evaluate.diff.primer.cvg | Evaluation of Coverage. |
| evaluate.fw.rev.combinations | Evaluation of Set Combinations |
| evaluate.GC.clamp | GC clamp |
| evaluate.primer.cvg | Evaluation of Primer Coverage. |
| evaluate.template.constraints | Evaluation of Template Constraints. |
| exclude.cols | Exclusion of Columns |
| filter.by.constraints | Filter By Constraints |
| filter.comparison.primers | Filter Multiple Primer Sets. |
| filterLimits-methods | Getter for Filtering Constraint Limits. |
| filter.primer.candidates | Filtering of Primer Candidates |
| filter_primers.by.Tm.delta | Filter by Melting Temperature Difference |
| filter.primer.set.opti | Filtering of Primers |
| filters-methods | Getter for Filtering Constraints. |
| fix_constraint_boundaries | Correction of Constraint Boundaries. |
| format.constraints | Format Constraint Names. |
| format.seq.ali | Format mismatches |
| format.seqs.tex | Format a Sequence for LateX output. |
| get.3prime.mismatch.pos | Identification of 3' Mismatches. |
| get.analysis.mode | Direction of Primers. |
| get.consensus.seq | Computation of Consensus. |
| get_constraint_deviation_data | Retrieve data for Constraint Deviations. |
| get.constraint.value.idx | Retrive Constraint Indices. |
| get.constraint.values | Get the Values of a Constraint. |
| get.coverage.matrix | Coverage Matrix |
| get.covered.templates | Covered Templates |
| get_covered.vanilla | Determination of the Covered Sequences. |
| get.cross.dimers | Cross dimers |
| get.cvg.constraint.settings | Gather all Coverage Constraints. |
| get.cvg.gain | Computation of Coverage Gain. |
| get_cvg_stats-list-method | Coverage Statistics for Multiple Primer Sets. |
| get_cvg_stats-Primers-method | Coverage Statistics of a Primer Set. |
| get.delta.G | Change in Free Energy. |
| get.dimer.data | Retrieval of dimerization energies. |
| get.duplex.energies | Determination of the Free Binding Energy. |
| get.eval.cols | Retrieval of Evaluation Columns. |
| get.extension | Identification of File extension. |
| get.ILP.vars | Retrieval of ILP Decisions |
| get.init.file.name | File Name for Initialized Primers. |
| get.leader.exon.regions | Assign Binding Regions |
| get.leader.exon.regions.single | Individual Binding Annotation |
| get.matches | Identification of Sequence Matches. |
| get_max_set_coverage | Determination of Maximal Coverage. |
| get.melting.temp.diff | Computation of Maximal Melting Temperature Differences. |
| get.merge.idx | Indices for merging sequences |
| get.missing.df | Uncovered Templates. |
| get.ORFs | Identification of ORFs. |
| get.other.constraint.settings | Gather all Other Constraints (for Shiny frontend). |
| get.PCR.settings | Gather all PCR settings. |
| get.plot.height | Plot Extent |
| get_plot_primer_data | Data for Primer Plot. |
| get.primer.binding.idx | Retrieval of Allowed Binding Indices. |
| get_primer_cvg_mm_plot_df | Data for Mismatch Primer Coverage Plot. |
| get.primer.identifier.string | Primer Identifier Creation. |
| get.redundant.cols | Identification of Redudant Primers. |
| get.relative.binding.pos | Retrieval of Relative Binding Positions. |
| get_report_fname | Creation of a Filename for Reports. |
| get.run.names | Getter for Run Names. |
| get.self.dimers | Self dimerization |
| get.sets.from.decisions | Optimal Sets from Decision Variables |
| get.static.tool.info | Retrieval of Tool Information. |
| get_template_cvg_data | Retrieval of Template Coverage Data. |
| get.tree.seqs | Determine Tree Consensus Sequences |
| get.unlist.idx | Index for Unlisting. |
| hclust.tree | Hierarchical Clustering. |
| highlight.mismatch | Highlight mismatches |
| html.format.structure | Formats a Dimerization Structure for HTML. |
| I.cvg | Primer Coverage. |
| ILPConstrained | Construct Coverage ILP. |
| initialize.primer.set | Creation of Initial Primers |
| Input | Input Functionalities. |
| insert_str | String Insertion. |
| interleave | Interleave strings Combines the input vectors in an... |
| J.cvg | Template Coverage. |
| joule.to.cal | Conversion from J to cal |
| listToXml | List to XML |
| merge.ambig.primers | Merge similar primers |
| merge.binding.information | Merge of Forward/Reverse Binding Information. |
| merge.primer.entries | Merge similar primers |
| merge.primer.entries.single | Merge input sequences |
| merge.select | Select merge indices |
| merge.template.decisions | Merge Template Decisions. |
| mismatch.info | Information about Mismatches. |
| mismatch.mutation.check | Identification of Mutations Induced by Mismatch Binding... |
| mismatch.string.to.list | Conversion of Mismatch Postions String to List. |
| modify.col.rep | Modification of Column Names. |
| my.disambiguate | Disambiguation of Sequences. |
| my.error | Custom Error |
| my_ggsave | Wrapper for the ggplot2::ggsave function. |
| my_rbind | Smartbind preserving classes. |
| my.read.fasta | Read FASTA File. |
| my.warning | Custom Warning. |
| nbr.of.repeats | Number of Repeats |
| nbr.of.runs | Number of Runs |
| openPrimeR-package | Multiplex PCR Primer Design and Analysis. |
| optiLimits-methods | Getter for Optimization Constraint Limits. |
| opti-methods | Getter for Optimization Constraints. |
| optimize.ILP | Solver for ILP Set Cover |
| optimize.primer.cvg | Greedy Optimization |
| optimize.template.binding.regions.dir | Optimization of Binding Regions |
| optimize.template.binding.regions.single | Optimization of Template Binding |
| Output | Output Functionalities. |
| pair_primers | Pairing of Forward and Reverse Primers. |
| parse.constraints | Parse XML Constraint Data. |
| parse.header | Parse FASTA headers |
| parse.IMGT.gene.groups | Parser for IMGT Groups. |
| parse.oligo.results | Parser for OligoArrayAux Dimerization Data. |
| plot.all.cvg.info | Plots Coverage Information |
| plot.all.filtering.stats | Plot Filtering Stats. |
| plot_constraint_deviation-list-method | Plot of Constraint Deviations for Multiple Primer Sets. |
| plot_constraint_deviation-Primers-method | Plot of Constraint Deviations for a Single Primer Set. |
| plot_constraint_fulfillment-list-method | Comparison of Evaluation Results. |
| plot_constraint_fulfillment-Primers-method | Overview of Constraint Fulfillment. |
| plot_constraint.histogram | Histogram of Constraints. |
| plot_constraint.histogram.nbr.mismatches | Histogram of Number of Mismatches. |
| plot_constraint.histogram.primer.efficiencies | Histogram of Efficiencies |
| plot_constraint-list-method | Boxplot for Comparing Constraints. |
| plot_constraint-Primers-method | Histogram of Constraint Values. |
| plot_cvg_constraints-list-method | Plot for Comparing Primer Coverage Constraints. |
| plot_cvg_constraints-Primers-method | Histogram of Coverage Constraints. |
| plot.Delta.DeltaG | Delta DeltaG Plot |
| plot.dimer.dist | Plot Dimer DeltaG |
| plot.excluded.hist | Plot of Excluded Primers |
| plot.filtering.runtime | Plot Filtering Runtimes |
| plot.filtering.stats | Plot of Overall Filtering Stats. |
| plot.filtering.stats.cvg | Plot of Filtering Stats for Coverage. |
| plot_primer_binding_regions-list-list-method | Plot of Primer Binding Regions for Multiple Sets. |
| plot_primer_binding_regions-Primers-Templates-method | Plot of Primer Binding Regions for a Single Primer Set. |
| plot_primer.comparison.box | Boxplot for Primer Comparison |
| plot_primer.comparison.mismatches | Plot Primer Mismatches |
| plot_primer_cvg-list-list-method | Plot Multiple Primer Coverages. |
| plot_primer_cvg_mismatches | Plot of Individual Primer Coverage and Mismatches. |
| plot_primer_cvg-Primers-Templates-method | Plot Individual Primer Coverage. |
| plot_primer_cvg_unstratified | Plot Individual Primer Coverage. |
| Plots | Plotting Functions. |
| plot_template_cvg_comparison_mismatch | Templates Coverage for Multiple Primer Sets. |
| plot_template_cvg_comparison_unstratified | Templates Coverage for Multiple Primer Sets. |
| plot_template_cvg-list-list-method | Templates Coverage for Multiple Primer Sets. |
| plot_template_cvg_mismatches | Bar Plot of Template Coverage for Mismatches. |
| plot_template_cvg-Primers-Templates-method | Bar Plot of Template Coverage. |
| plot_template_cvg_unstratified | Bar Plot of Template Coverage. |
| plot_template_structure | Plot of Template Folding Energies. |
| pos.to.range | Conversion of Positions to Ranges. |
| predict_coverage | Prediction of Primer Coveragee. |
| prefilter.primer.candidates | Identication of Short Primers. |
| prepare.constraint.plot | Preparation of Comparison Plot for Evaluation. |
| prepare.dimer.seqs | Preparation of Input for Dimerization. |
| prepare_mm_plot | Data Preparation for Mismatch Plot. |
| prepare_template_cvg_mm_data | Preparation of Data for Plotting Mismatch Template Coverage. |
| primer.binding.regions.data | Primer Binding Region Data |
| primer.coverage.for.groups | Determination of Primer Coverage for Groups. |
| PrimerDesign | Primer Design Functionalities. |
| PrimerEval | Primer Evaluation. |
| primer.set.parameter.stats | Primer Set Statistics |
| Primers-method | S4 cbind for Primers. |
| rbind.primer.data | Rbind for Primer Data Frames. |
| rbind.Primers | rbind for Primers class. |
| rbind.Templates | rbind for Template class. |
| read.leaders | Read Individual Binding Regions |
| read_primers_csv | Read Primer CSV File. |
| read_primers.internal | Internal Function for Reading Primers |
| read_primers_multiple | Input of Multiple Primer Sets. |
| read.secondary.structure.raw | Read a Secondary Structure |
| read.sequences | Read Sequences. |
| read_templates_csv | Read Template CSV File |
| read_templates_fasta | Input of Template Sequences. |
| read_templates_multiple | Input of Multiple Templates. |
| read_templates_single | Input of a Single Template File. |
| relax.constraints | Relaxation of Constraints |
| relax.opti.constraints | Relaxation of Optimization Constraints |
| remove.redundant.cols | Removal of Redundant Primers. |
| remove.seqs.by.keyword | Removal of Partial Sequences. |
| rename.constraint.options | Renaming of Constraint Options. |
| render_report | Renders an rmarkdown file using Pandoc. |
| reorder.primer.table | Reorder Primers |
| restriction_ali | Identification of Badly Fitting Regions. |
| restriction_hits | Identification of Restriction Sites. |
| restriction_match | Identification of Sequence Matches. |
| retrieve.leader.region | Retrieval of Binding Regions |
| rev.comp.sequence | Reverse complement of a sequence |
| rev.sequence | Reversion of a sequence |
| runTutorial | The openPrimeR Tutorial. |
| sanitize_path | Sanitiziation of Filename. |
| score.conservation | Conservation Scores |
| Scoring | Scoring Functions. |
| select.allowed.binding.events | Selection of Binding Events |
| select_best_binding | Selection of Best (smallest number of mismatches) Binding... |
| select.best.ILP | Selection of Best ILP |
| select.best.opti.result | Selection of Best Greedy Result |
| select.best.primer.idx | Greedy Choice |
| select.best.primer.set | Selection of Best Primer Set. |
| select.binding.events | Selection of Individual Binding Events |
| select.constraints | Selection of Constraints. |
| select.min.cross.idx | Selection of cross dimer index |
| select.primer.region.by.conservation | Selection by Conservation |
| select.primers.by.cvg | Greedy Optimization. |
| selenium.installed | Determination if Selenium is installed. |
| set.new.constraint.value | Update Constraint Settings. |
| set.new.limits | Relaxation of Constraint Limits. |
| Settings | Settings Functionalities. |
| shannon.entropy | Shannon Entropy |
| solve.ILP | Solve an ILP |
| split_str_by_index | Split a sequence |
| stats_plot_data | Combination of Filtering Stats. |
| store.filtering.sets | Writes Filtering Data Sets to Disk. |
| string.list.format | Format a String List. |
| string.list.format.total | Format Strings |
| string.to.IQR | Conversion of Comma-Separated String to IQR String |
| subset.ILP | Subset ILP Constructor |
| TemplatesFunctions | Template Functionalities. |
| Templates-method | S4 cbind for Templates. |
| ungap_sequence | Ungapping of Sequences. |
| unify.leaders | Unification of Leaders |
| update.binding.ranges.by.conservation | Updates Binding Region in the Alignment by conservation. |
| update.binding.regions | Update of Binding Regions. |
| update.constraint.values | Update of Primer Constraints. |
| update.cvg.data | Update Coverage Information. |
| update.individual.binding.region | Adjustment of Existing Binding Regions for one Direction. |
| update.opti.results | Augmentation of Optimized Primer Data. |
| update_primer_binding_regions | Update of Primer Binding Regions. |
| update_primer_cvg | Updates the Primer Coverage. |
| validate_primers | Validates a Primers Object. |
| validate_templates | Validates a Template Object. |
| view.cvg.primers | View the Evaluated Primers. |
| view.dimer.df | Formatted dimerization data. |
| view.input.primers | View the Input Primers. |
| view.primers | View the Evaluated Primers. |
| view.primers.report | View the Evaluated Primers in the Report. |
| visualize.all.results | Visualization of Design Results. |
| visualize.filtering.results | Visualization of Filtering Results. |
| were.constraints.relaxed | Check for Relaxation |
| write.out.primer.info | Write Out Optimization Data |
| xmlToChar | Conversion of XML to Character. |
