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

## Documentation for package ‘hiReadsProcessor’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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/sff 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