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


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Documentation for package ‘hiReadsProcessor’ version 1.43.0

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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