Man pages for KasperThystrup/circulaR
Characterization of circRNAs from Total RNA-seq data
| addFilter | Add filter to bsj.read-data. |
| addKnownJunctions | Function to add information on annotated junctions and... |
| addLinCounts | Add information on usage of donor and acceptor sites for... |
| adjustAlignment | Read alignment to nearest genes |
| alignmentStats | Extract alignment stats |
| annotateByOverlap | Annotate circRNAs (bsID) by identifying overlapping genes |
| bam.file | Accessor for the BAM file path |
| bam.file-set | Replacement method for the BAM file path |
| bsid2bed | Convert bsID to BED like format. |
| bsid2gr | Convert bsID to GRanges object |
| bsid2junc | Convert bsID to GRanges object of acceptor or donor positions |
| bsj.counts | Accessor for the backsplice junction count data |
| bsj.counts-set | Replacement method for the backsplice junction count data |
| bsjExonStats | Calculate exon statistics |
| bsj.reads | Accessor for the backsplice junction read data |
| bsj.reads-set | Replacement method for the backsplice junction read data |
| bsjStats | Make summary statistics of the chimeric/backspliced reads. |
| BSJTrack | Create track of backsplice sites |
| bsReadCoverage | Determine coverage of backspliced reads. |
| c2l.ratio | Function to calculate the circular to linear ratio for a... |
| calcCoverage | Function to calculate coverage of backspliced reads |
| categorizeBSJ | Function to categorize backsplice sites |
| checkChimFile | Function to test if Chimeric.out.junction file can be read... |
| checkInputFiles | Check if amount of input files are correct, and notify if any... |
| checkPEReads | Check if both mates of a read pair are consistent with the... |
| checkPEReads_old | Check if both mate pairs are consistent with backsplice... |
| checkVariables | A error message generator, for checking classes of variables... |
| chim.file | Accessor for the chimeric file path |
| chim.file-set | Replacement method for the chimeric file path |
| cigar2covr | Function to return covered chromosomal positions from a start... |
| circExperiment-class | S4 class for representing an experiment consisting of... |
| circSample | S4 class for storing circRNA relevant information. |
| circulaR | circulaR pipeline wrapper |
| compareToKnownJunctions | Compare backsplice junction identified by STAR to junction... |
| constructBsId | Construct unique backsplice junction IDs |
| constructSJDB | Construct a database of known splice junctions from a... |
| count.file | Accessor for the linear read count data file path |
| count.file-set | Replacement method for the linear read count data file path |
| countSumChimFile | Summarize the read count for each backsplice junction |
| determineAmbiguousHits | Analyses the provided donors and acceptors to determine if... |
| exp.mat | Accessor for expression data from circExperiment |
| findNearest | Candidate backsplice data are split into donors and acceptors... |
| firstread.firststrand | Accessor for the strandedness protocol of sample library... |
| firstread.firststrand-set | Replacement method for the strandedness protocol of sample... |
| gb | Accessor for genome build |
| gb-set | Replacement method for genome build |
| generateJunctionMotifs | Generate junction motifs |
| getCandidateBackspliceSites | Read candidate backsplice sites from Chimeric.out.junction... |
| getKnownJunctions | Generate database of known splice junction sites from a TxDb-... |
| guessPE | Guess whether data are paired ended or not by parsing the BAM... |
| indexJunctions | FURTHER FUNCTIONALITY should be implemented if we wish to... |
| inferExons | Infer the exons structure of a circular RNA |
| is.empty | Check for empty values |
| junctionMotif | Extract junction motif(s) from genome |
| junctionsToGRanges | Simple wrapper for generating a GRanges object, it supports... |
| knownJunctionInRepeatRegion | Function to identify chimeric reads eligible for shifting |
| knownJunctionSites | Determine whether reads in a bsj.read-table uses known splice... |
| label | Accessor for sample label |
| label-set | Replacement method for sample label |
| locateSamples | Method for automatically detecting and setting up all samples... |
| log.file | Accessor for the STAR alignment Log file path |
| log.file-set | Replacement method for the STAR alignment Log file path |
| lsj.counts | Accessor for summarized data on linear splice sites |
| lsj.counts-set | Replacement method for summarized data on linear splice sites |
| name | Accessor for experiment name circExperiment class accessors... |
| name-set | Replacement method for experiment name |
| paired.end | Accessor for the library preparation protocol realtive to... |
| paired.end-set | Replacement method for the library preparation protocol... |
| parseCIGAR | #' Construct bsID from genomic coordinates #' #' @param gb... |
| parseDataDir | Parse a directory to identify samples for processing in the... |
| path | Accessor for main directory path circExperiment class... |
| plotAll | Make homemade sashimi plot |
| plotBSJ | Plot backsplice junctions stored in a GRanges object. |
| plotBSJrepeats | Zoomed in view of the donor and acceptor sites |
| plotCoverage | Function to plot coverage as barplot. |
| plotSJ | Plot linear splice sites stored in a GRanges object. |
| plotTxModels | Plot transcript models. |
| plotTxModelsOLD | Plot transcripts stored in a TxDB. |
| pruneChromosomes | Prune chromosomes |
| readBSJdata | Read the chimeric data of a circSample or circExperiment. |
| readChimFile | Wrapper for easy reading of Chimeric.out.junction file |
| readLSJdata | Read the data on reads spanning linear splice junctions |
| rescueAmbiguous | The function used to identify nearest known junction... |
| resolveReads | Compares the full backsplice candidate set with reads that... |
| sample.id | Accessor for sample.id |
| sample.id-set | Replacement method for sample.id |
| samples-circExperiment-method | Accessor for experiment samples |
| samples-set | Replacement method for samples |
| shiftAlignment | Function to shift alignment to overlap with known junctions |
| sj.file | Accessor for the Linear splice junctions file path |
| sj.file-set | Replacement method for the Linear splice junctions file path |
| SJTrack | Create a track of linear splice junction |
| STARlogParser | Read and parse Log.final.out file |
| summarizeBSJreads | Summarize number of reads per backsplice junction. |
| swapStrands | Reverse strand information and donor/acceptor order, in the... |
| vizJunctions | Visualize the linear and backsplice junction of a specific... |
| wrapperFunction | Process Chimeric.out.junction file(s) to identify and... |
