Man pages for philliplab/MotifBinner2
Processes NGS Primer ID Datasets
| alignBins | Removes sequences shorter than a given cutoff |
| alignBins_internal | aligns fwd and rev sequences to a profile |
| alignBinsMSA | Removes sequences shorter than a given cutoff |
| alignBinsMSA_internal | aligns fwd and rev sequences to a profile |
| alignBinsSP | Removes sequences shorter than a given cutoff |
| alignBinsSP_internal | aligns fwd and rev sequences to a profile |
| allResults | Performs any final processing operations |
| ambigSeqs | Removes sequences with too many ambig bases |
| apply_consensus_cutoff | Applies the consensus cutoff to an existing consensuses file |
| applyOperation | Applies a single operation |
| basicQC | Performs basic quality assessment |
| binSeqErr | Computes the sequencing parameters for each bin |
| binSeqErr_internal | Computes the sequencing error rate for each bin |
| binSizeCheck | Removes sequences shorter than a given cutoff |
| blastTrim | Removes sequences shorter than a given cutoff |
| buildConfig | Builds the overlapping or non-overlapping production configs |
| buildConfig_nol_test | Test config builder for non-overlapping reads |
| buildConfig_ol_prod | Builds the config for overlapping reads - stable version |
| buildConsensus | Removes sequences shorter than a given cutoff |
| build_cutoff_models | Builds the consensus cutoff models given a dataset index file |
| computeMetrics | Computes metrics useful for reporting |
| dataTracing | Removes sequences shorter than a given cutoff |
| doubleClusterTally | Tallies to true sizes of clusters of clusters |
| extractData | Extracts required dataset by navigating down into a list |
| extractPIDs | Extracts the PIDs after affixes were trimmed and add then to... |
| genKeptVector | Generates a vector of T/F indicating which sequences were... |
| genReport | Generates a report for a operation or the full process |
| genSummary | Generates a summary for a operation or the full process |
| genSummary_case1 | Generates summary table when there is one trim step with one... |
| genSummary_case3 | Generates summary table when there is one trim step with many... |
| genSummary_case4 | Generates summary table when there is many trim steps each... |
| get_consensus_cutoff | Returns the consensus cutoff to use based on a given models... |
| get_cutoff_models | Returns a data.frame of the stored models |
| getKept | Get the data kept after a trimming step |
| getTrimmed | Get the data trimmed at a trimming step |
| group_cons_bins_internal | Group consensus sequences and their read together |
| kable_summary | formats a summary table for markdown |
| loadData | Loads a fastq file |
| makeIUPACScoreMat | This function creates a scoring matrix for aligning IUPAC... |
| make_monotonic | Makes a series of numbers monotonically increasing or... |
| matchPairs | Removes sequences shorter than a given cutoff |
| mergePEAR | Removes sequences shorter than a given cutoff |
| moving_statistic | Computes a moving statistic over a sliding window. |
| mutate_letter | Mutates a nucleotide to another |
| pairwiseMSA | Generates a MSA relative to a profile without any inserts... |
| plot_consensus_cutoff_model | Plots a consensus cutoff model |
| plot_consensus_cutoff_sim | Plots the results of a consensus_cutoff simulation |
| prepConfig | Prepares config list for inclusion in final report |
| primerDimer | Removes perimer-dimer sequences (based on sequence length) |
| primerSeqErr | Removes sequences shorter than a given cutoff |
| processBadPIDs | Removes sequences shorter than a given cutoff |
| processPrimers | Processes a dataset with Primer IDs |
| qualTrim | Removes sequences that does not match specified quality |
| reformat_tallies | Reformats the tallies produced by tallyPrimerSeqError_cpp |
| regionSplit | Removes sequences shorter than a given cutoff |
| removeChars | Removes all instances of a specified character from a set of... |
| saveToDisk | Save the relevant results of an operation to disk |
| seqLength | Removes sequences shorter than a given cutoff |
| shortReadQ_forced_append | Forces ShortReadQ objects to append into a single ShortReadQ... |
| sim_all_parents_main_off | Simulate range of parents and their main offspring sizes |
| sim_one_parent_main_off | Simulate a parent and its main offspring size |
| sim_wrapper | Wrapper that performs simulation and process the results |
| sliceTime | Internal function that reforms a list storing exe times |
| timingTable | Produces the timing tables in the reports |
| trimAffixes | Trims the ends of the sequences so that they all start at the... |
| vsearchCluster | Removes sequences shorter than a given cutoff |
