InternalFunctions {EventPointer} | R Documentation

## EventPointer Internal Functions

### Description

Internal functions used by EventPointer in the different steps of the algorithm

### Usage

    annotateEvents(Events, PSR_Gene, Junc_Gene, Gxx)

    annotateEventsMultipath(Events, PSR_Gene, Junc_Gene, Gxx, paths)

    AnnotateEvents_RNASeq(Events)

    AnnotateEvents_RNASeq_MultiPath(Events, paths)

    AnnotateEvents_KLL(Events, Gxx, GenI)

    ClassifyEvents(SG, Events, twopaths)

    estimateAbsoluteConc(Signal1, Signal2, SignalR, lambda)

    estimateAbsoluteConcmultipath(datos, lambda = 0.1)

    findTriplets(randSol, tol = 1e-08)

    findTriplets2(Incidence, paths = 2, randSol)

    GetCounts(Events, sg_txiki, type = "counts")

    GetCountsMP(Events, sg_txiki, type = "counts")

    getEventPaths(Events, SG)

    getEventMultiPaths(Events, SG, twopaths, paths)

    GetIGVPaths(EventInfo, SG_Edges)

    getPSI(ExFit, lambda = 0.1)

    getPSI_RNASeq(Result, lambda = 0.1)

    getPSI_RNASeq_MultiPath(Result, lambda = 0.1)

    getRandomFlow(Incidence, ncol = 1)

    IHsummarization(Pv1, t1, Pv2, t2, coherence = "Opposite")

    pdist2(X, Y)

    PrepareCountData(Result)

    PrepareProbes(Probes, Class)

    PrepareOutput(Result, Final)

    SG_Info(SG_Gene)

    SG_creation(SG_Gene)

    SG_creation_RNASeq(SG_Gene)

    WriteGTF(PATH, Data, Probes, Paths)

    WriteGTF_RNASeq(PATH, Data, Paths)

    flat2Cdf(file, chipType, tags = NULL, rows = 2560, cols = 2560,
      verbose = 10, xynames = c("X", "Y"), gcol = 5, ucol = 6,
      splitn = 4, col.class = c("integer", "character")[c(1, 1, 1, 2, 2,
      2)], Directory = getwd(), ...)

    uniquefast(X)

    filterimagine(Info, paths)

    transfromedge(SG, SG_Gene)

    sacartranscritos(edgetr, events)

    convertToSGFeatures2(x, coerce = FALSE, merge = FALSE)

    processFeatures2(features, coerce = FALSE, merge = FALSE)

    annotate2(query, subject)

    annotateFeatures2(query, subject)

    mergeExonsTerminal2(features, min_n_sample = 1)

    get_beta(combboots, incrPSI_original, ncontrastes)

    get_table(PSI_arrayP, nevents, totchunk, chunk, nsamples, incrPSI_original,
      V, nboot, nbootin, ncontrastes)

    get_YB(PSI_arrayS, l, nsamples, I, J, CTEind)

    getInfo(table, ncontrast)

    PrimerSequenceGeneral(taqman, FinalExons, generaldata, SG, Dir, nPrimers,
      Primer3Path = Sys.which("primer3_core"), maxLength, minsep, wminsep,
      valuethreePpenalty, wnpaths, qualityfilter)

    PrimerSequenceTwo(FinalExons, SG, generaldata, n, thermo.param,
      Primer3Path, settings)

    ProbesSequence(SG, FinalSeq, generaldata, Dir,
      Primer3Path = Sys.which("primer3_core"), nProbes)

    sort.exons(namesPath, decreasing = FALSE)

    all_simple_paths2(wg, from, to, ...)

    callPrimer3(seq, threeprimers = FALSE, pr, reverse = FALSE,
      size_range = "150-500", Tm = c(57, 59, 62), name = "Primer1",
      Primer3Path = "primer3-2.3.7/bin/primer3_core",
      thermo.param = "primer3-2.3.7/src/primer3_config/",
      sequence_target = NULL,
      settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt")

    callPrimer3probes(seq, name = "Primer1",
      Primer3Path = "primer3-2.3.7/bin/primer3_core",
      thermo.param = "primer3-2.3.7/src/primer3_config/",
      sequence_target = NULL,
      settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt")

    CreateSequenceforProbe(SG, Exons, FinalSeq, n)

    findPotencialExons(D, namesPath, maxLength, SG, minexonlength)

    fullExons(namesPath)

    includeaexons(Forward)

    genreverse(FinalInfo)

    getDistanceseachPath(Exon1, Exon2, generaldata, distinPrimers, SG)

    getDominants2(PrimersTwo, Primers1, commonForward, commonReverse, namesRef,
      D, numberOfPaths, nprimerstwo, ED, wNpaths = 1000, wP12inRef = 1000)

    getDominantsFor(Primers1, Primers2, commonForward, namesRef, D,
      numberOfPaths, Event, ncommonForward, ED, wNpaths = 1000,
      wP12inRef = 1000)

    getDominantsRev(Primers1, Primers2, commonReverse, namesRef, D,
      numberOfPaths, Event, ncommonReverse, ED, wNpaths = 1000,
      wP12inRef = 1000)

    getExonsFullSignal(namesPath, SG)

    getFinalExons(generaldata, maxLength, nPrimerstwo, ncommonForward,
      ncommonReverse, nExons, minsep, wminsep, valuethreePpenalty,
      minexonlength)

    getgeneraldata(SG, Event, shortdistpenalty)

    getrankexons(SG, Dominants, nt, wg, items, minsep, wminsep,
      valuethreePpenalty, D)

    getranksequence(taqman, Fdata, maxLength, minsep, wminsep,
      valuethreePpenalty, wnpaths, qualityfilter)

    PrimerSequenceCommonFor(FinalExons, SG, generaldata, n, thermo.param,
      Primer3Path, settings)

    PrimerSequenceCommonRev(FinalExons, SG, generaldata, n, thermo.param,
      Primer3Path, settings)

### Value

Internal outputs

[Package EventPointer version 2.4.0 Index]