Man pages for malnirav/hiReadsProcessor
Functions to process LM-PCR reads from 454/Illumina data

addFeatureAdd a specific feature/attribute to the sampleInfo object.
addListNameToReadsPrepend name attribute of a list to DNAStringSet
annotateSitesFind the 5' primers and add results to SampleInfo object.
blatListedSetAlign a listed DNAStringSet to a reference using gfClient or...
blatSeqsAlign sequences using BLAT.
chunkizeBreaks an object into chunks of N size.
clusterSitesCluster/Correct values within a window based on their...
crossOverCheckRemove values/positions which are overlapping between...
dereplicateReadsRemoves duplicate sequences from DNAStringSet object.
doRCtestTest if pattern aligns better in +/- orientation.
extractFeatureExtract a specific feature/attribute of the sampleInfo...
extractSeqsExtract sequences for a feature in the sampleInfo object.
findAndRemoveVectorFind and trim vector sequence from reads.
findAndTrimSeqFind and trim a short pattern sequence from the subject.
findBarcodesDemultiplex reads by their barcodes
findIntegrationsFind the integration sites and add results to SampleInfo...
findLinkersFind the 3' linkers and add results to SampleInfo object.
findLTRsFind the 5' LTRs and add results to SampleInfo object.
findPrimersFind the 5' primers and add results to SampleInfo object.
findVectorFind vector DNA in reads and add results to SampleInfo...
getIntegrationSitesObtain integration sites from BLAT output
getSectorsForSamplesGet sectors for samples defined in the sampleInfo object.
getSonicAbundCalculate breakpoint/sonic abundance of integration sites in...
hiReadsProcessorFunctions to process LM-PCR reads from 454/Illumina data
isuSitesBin values or make ISUs by assigning a unique ID to them...
otuSitesBin values or make OTUs by assigning a unique ID to them...
pairUpAlignmentsPair up alignments in a GRanges object
pairwiseAlignSeqsAlign a short pattern to variable length target sequences.
primerIDAlignSeqsAlign a short pattern with PrimerID to variable length target...
pslPSL file output
pslColsReturn PSL file columns with classes
pslToRangedObjectConvert psl dataframe to GRanges
read.BAMasPSLReads a BAM/SAM file and converts it into a PSL like format.
read.blast8Read blast8 file(s) outputted by BLAT
read.pslRead PSL file(s) outputted by BLAT
read.sampleInfoRead a sample information file and format appropriate...
read.SeqFolderRead contents of a sequencing folder and make a SimpleList...
read.seqsFromSectorRead fasta/fastq/sff given the path or sampleInfo object.
removeReadsWithNsRemove sequences with ambiguous nucleotides.
replicateReadsReplicate sequences from DNAStringSet object using counts...
sampleSummarySimple summary of a sampleInfo object.
seqPropsSample Integration Sites Sequencing Data
splitByBarcodeSplit DNAStringSet object using first X number of bases...
splitSeqsToFilesSplit DNA sequences into smaller files.
startgfServerStart/Stop a gfServer instance
trimSeqsTrim sequences from a specific side.
troubleshootLinkersCompare LTRed/Primed sequences to all linkers.
vpairwiseAlignSeqsAlign a short pattern to variable length target sequences.
write.listedDNAStringSetWrite a fasta file per sample in parallel
write.pslWrite PSL file from dataframe or GRanges
malnirav/hiReadsProcessor documentation built on Sept. 17, 2017, 10:56 a.m.