Processes NGS Primer ID Datasets

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Documentation for package ‘MotifBinner2’ version 0.0.5

• DESCRIPTION file.

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alignBins	Removes sequences shorter than a given cutoff
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
alignBins_internal	aligns fwd and rev sequences to a profile
allResults	Performs any final processing operations
ambigSeqs	Removes sequences with too many ambig bases
applyOperation	Applies a single operation
apply_consensus_cutoff	Applies the consensus cutoff to an existing consensuses file
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 the sequence names
genKeptVector	Generates a vector of T/F indicating which sequences were kept or trimmed.
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 value
genSummary_case3	Generates summary table when there is one trim step with many values
genSummary_case4	Generates summary table when there is many trim steps each with many values
getKept	Get the data kept after a trimming step
getTrimmed	Get the data trimmed at a trimming step
get_consensus_cutoff	Returns the consensus cutoff to use based on a given models file
get_cutoff_models	Returns a data.frame of the stored models
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 sequences
make_monotonic	Makes a series of numbers monotonically increasing or decreasing
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 into the profile
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 sequences
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 object
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 same place
vsearchCluster	Removes sequences shorter than a given cutoff