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 |