Man pages for malnirav/hiReadsProcessor
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... |
| 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 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 |
