Functions to process LM-PCR reads from 454/Illumina data

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Documentation for package ‘hiReadsProcessor’ version 1.43.0

• DESCRIPTION file.
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hiReadsProcessor-package	Functions to process LM-PCR reads from 454/Illumina data
addFeature	Add a specific feature/attribute to the sampleInfo object.
addListNameToReads	Prepend name attribute of a list to DNAStringSet
annotateSites	Find the 5' primers and add results to SampleInfo object.
blatListedSet	Align a listed DNAStringSet to a reference using gfClient or standalone BLAT.
blatSeqs	Align sequences using BLAT.
chunkize	Breaks an object into chunks of N size.
clusterSites	Cluster/Correct values within a window based on their frequency given discrete factors
crossOverCheck	Remove values/positions which are overlapping between discrete groups based on their frequency.
decodeByBarcode	Demultiplex reads by their barcodes
dereplicateReads	Removes duplicate sequences from DNAStringSet object.
doRCtest	Test if pattern aligns better in +/- orientation.
extractFeature	Extract a specific feature/attribute of the sampleInfo object.
extractSeqs	Extract sequences for a feature in the sampleInfo object.
findAndRemoveVector	Find and trim vector sequence from reads.
findAndTrimSeq	Find and trim a short pattern sequence from the subject.
findBarcodes	Demultiplex reads by their barcodes
findIntegrations	Find the integration sites and add results to SampleInfo object.
findLinkers	Find the 3' linkers and add results to SampleInfo object.
findLTRs	Find the 5' LTRs and add results to SampleInfo object.
findPrimers	Find the 5' primers and add results to SampleInfo object.
findVector	Find vector DNA in reads and add results to SampleInfo object.
getIntegrationSites	Obtain integration sites from BLAT output
getSectorsForSamples	Get sectors for samples defined in the sampleInfo object.
getSonicAbund	Calculate breakpoint/sonic abundance of integration sites in a population
hiReadsProcessor	Functions to process LM-PCR reads from 454/Illumina data
isuSites	Bin values or make ISUs by assigning a unique ID to them within discrete factors.
otuSites	Bin values or make OTUs by assigning a unique ID to them within discrete factors.
pairUpAlignments	Pair up alignments in a GRanges object
pairwiseAlignSeqs	Align a short pattern to variable length target sequences.
primerIDAlignSeqs	Align a short pattern with PrimerID to variable length target sequences.
psl	PSL file output
pslCols	Return PSL file columns with classes
pslToRangedObject	Convert psl dataframe to GRanges
read.BAMasPSL	Reads a BAM/SAM file and converts it into a PSL like format.
read.blast8	Read blast8 file(s) outputted by BLAT
read.psl	Read PSL file(s) outputted by BLAT
read.sampleInfo	Read a sample information file and format appropriate metadata.
read.SeqFolder	Read contents of a sequencing folder and make a SimpleList object
read.seqsFromSector	Read fasta/fastq given the path or sampleInfo object.
removeReadsWithNs	Remove sequences with ambiguous nucleotides.
replicateReads	Replicate sequences from DNAStringSet object using counts identifier or vector
sampleSummary	Simple summary of a sampleInfo object.
seqProps	Sample Integration Sites Sequencing Data
splitByBarcode	Split DNAStringSet object using first X number of bases defined by a vector.
splitSeqsToFiles	Split DNA sequences into smaller files.
startgfServer	Start/Stop a gfServer instance
stopgfServer	Start/Stop a gfServer instance
trimSeqs	Trim sequences from a specific side.
troubleshootLinkers	Compare LTRed/Primed sequences to all linkers.
vpairwiseAlignSeqs	Align a short pattern to variable length target sequences.
write.listedDNAStringSet	Write a fasta file per sample in parallel
write.psl	Write PSL file from dataframe or GRanges