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

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Author
Nirav V Malani <malnirav@gmail.com>
Date of publication
None
Maintainer
Nirav V Malani <malnirav@gmail.com>
License
GPL-3
Version
1.10.0

View on Bioconductor

Man pages

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...
blatSeqs
Align sequences using BLAT.
chunkize
Breaks an object into chunks of N size.
clusterSites
Cluster/Correct values within a window based on their...
crossOverCheck
Remove values/positions which are overlapping between...
dereplicateReads
Removes duplicate sequences from DNAStringSet object.
doRCtest
Test if pattern aligns better in +/- orientation.
extractFeature
Extract a specific feature/attribute of the sampleInfo...
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...
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...
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...
hiReadsProcessor
Functions to process LM-PCR reads from 454/Illumina data
isuSites
Bin values or make ISUs by assigning a unique ID to them...
otuSites
Bin values or make OTUs by assigning a unique ID to them...
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...
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...
read.SeqFolder
Read contents of a sequencing folder and make a SimpleList...
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...
sampleSummary
Simple summary of a sampleInfo object.
seqProps
Sample Integration Sites Sequencing Data
splitByBarcode
Split DNAStringSet object using first X number of bases...
splitSeqsToFiles
Split DNA sequences into smaller files.
startgfServer
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

Files in this package

hiReadsProcessor/.BBSoptions
hiReadsProcessor/.Rinstignore
hiReadsProcessor/DESCRIPTION
hiReadsProcessor/NAMESPACE
hiReadsProcessor/NEWS
hiReadsProcessor/R
hiReadsProcessor/R/hiReadsProcessor.R
hiReadsProcessor/README.md
hiReadsProcessor/build
hiReadsProcessor/build/vignette.rds
hiReadsProcessor/data
hiReadsProcessor/data/FLX_seqProps.RData
hiReadsProcessor/data/psl.RData
hiReadsProcessor/inst
hiReadsProcessor/inst/doc
hiReadsProcessor/inst/doc/Tutorial.R
hiReadsProcessor/inst/doc/Tutorial.Rmd
hiReadsProcessor/inst/doc/Tutorial.html
hiReadsProcessor/inst/extdata
hiReadsProcessor/inst/extdata/FLX_sample_run
hiReadsProcessor/inst/extdata/FLX_sample_run/RunData
hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/1.TCA.454Reads.fna.gz
hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/2.TCA.454Reads.fna.gz
hiReadsProcessor/inst/extdata/FLX_sample_run/RunData/3.TCA.454Reads.fna.gz
hiReadsProcessor/inst/extdata/FLX_sample_run/Vectors
hiReadsProcessor/inst/extdata/FLX_sample_run/Vectors/HIV1.fa
hiReadsProcessor/inst/extdata/FLX_sample_run/Vectors/MLV-vector.fa
hiReadsProcessor/inst/extdata/FLX_sample_run/sampleInfo.xlsx
hiReadsProcessor/inst/tests
hiReadsProcessor/inst/tests/runTests.R
hiReadsProcessor/inst/tests/tests
hiReadsProcessor/inst/tests/tests/test_coreFeatures.R
hiReadsProcessor/man
hiReadsProcessor/man/addFeature.Rd
hiReadsProcessor/man/addListNameToReads.Rd
hiReadsProcessor/man/annotateSites.Rd
hiReadsProcessor/man/blatListedSet.Rd
hiReadsProcessor/man/blatSeqs.Rd
hiReadsProcessor/man/chunkize.Rd
hiReadsProcessor/man/clusterSites.Rd
hiReadsProcessor/man/crossOverCheck.Rd
hiReadsProcessor/man/dereplicateReads.Rd
hiReadsProcessor/man/doRCtest.Rd
hiReadsProcessor/man/extractFeature.Rd
hiReadsProcessor/man/extractSeqs.Rd
hiReadsProcessor/man/findAndRemoveVector.Rd
hiReadsProcessor/man/findAndTrimSeq.Rd
hiReadsProcessor/man/findBarcodes.Rd
hiReadsProcessor/man/findIntegrations.Rd
hiReadsProcessor/man/findLTRs.Rd
hiReadsProcessor/man/findLinkers.Rd
hiReadsProcessor/man/findPrimers.Rd
hiReadsProcessor/man/findVector.Rd
hiReadsProcessor/man/getIntegrationSites.Rd
hiReadsProcessor/man/getSectorsForSamples.Rd
hiReadsProcessor/man/getSonicAbund.Rd
hiReadsProcessor/man/hiReadsProcessor.Rd
hiReadsProcessor/man/isuSites.Rd
hiReadsProcessor/man/otuSites.Rd
hiReadsProcessor/man/pairUpAlignments.Rd
hiReadsProcessor/man/pairwiseAlignSeqs.Rd
hiReadsProcessor/man/primerIDAlignSeqs.Rd
hiReadsProcessor/man/psl.Rd
hiReadsProcessor/man/pslCols.Rd
hiReadsProcessor/man/pslToRangedObject.Rd
hiReadsProcessor/man/read.BAMasPSL.Rd
hiReadsProcessor/man/read.SeqFolder.Rd
hiReadsProcessor/man/read.blast8.Rd
hiReadsProcessor/man/read.psl.Rd
hiReadsProcessor/man/read.sampleInfo.Rd
hiReadsProcessor/man/read.seqsFromSector.Rd
hiReadsProcessor/man/removeReadsWithNs.Rd
hiReadsProcessor/man/replicateReads.Rd
hiReadsProcessor/man/sampleSummary.Rd
hiReadsProcessor/man/seqProps.Rd
hiReadsProcessor/man/splitByBarcode.Rd
hiReadsProcessor/man/splitSeqsToFiles.Rd
hiReadsProcessor/man/startgfServer.Rd
hiReadsProcessor/man/trimSeqs.Rd
hiReadsProcessor/man/troubleshootLinkers.Rd
hiReadsProcessor/man/vpairwiseAlignSeqs.Rd
hiReadsProcessor/man/write.listedDNAStringSet.Rd
hiReadsProcessor/man/write.psl.Rd
hiReadsProcessor/vignettes
hiReadsProcessor/vignettes/Tutorial.Rmd
hiReadsProcessor/vignettes/hiReadsProcessor_object.png
hiReadsProcessor/vignettes/hiReadsProcessor_workflow.png