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")

    getPathCounts(x, readsC, widthinit)

    getPathFPKMs(x, readsC, widthinit)

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

    getPathCountsMP(x, readsC, widthinit)

    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)

    SG_creation_fast(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)

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

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

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

    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, mygenomesequence)

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

    fullExons(namesPath)

    includeaexons(Forward)

    genreverse(FinalInfo, taqman)

    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,
      mygenomesequence
    )

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

    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)

    checkContrastDesignMatrices(C, D)

    mclapplyPSI_Bootstrap(
      PSI_boots,
      Design,
      Contrast,
      cores,
      ram,
      nbootstraps,
      KallistoBootstrap,
      th,
      verbose = 0
    )

    call_get_table_Bootstrap(
      chunklist,
      Design,
      Contrast,
      nbootstraps,
      KallistoBootstrap,
      th,
      cores
    )

    get_table_Bootstrap(
      PSI_arrayP,
      Design,
      Contrast,
      nbootstraps,
      KallistoBootstrap,
      th
    )

    pvalue_incr_PSI(incr_PSI, th = 0, verbose = 0)

    calculateCorrelationTest(A, B, method = c("pearson", "spearman"))

    x %in2% table

    callGRseq_parallel(EventsFound, SG_List, cores, typeA, nt)

    getpij(A)

    speedglm.wfit2(
      y,
      X,
      intercept = TRUE,
      weights = NULL,
      row.chunk = NULL,
      family = gaussian(),
      start = NULL,
      etastart = NULL,
      mustart = NULL,
      offset = NULL,
      acc = 1e-08,
      maxit = 25,
      k = 2,
      sparselim = 0.9,
      camp = 0.01,
      eigendec = TRUE,
      tol.values = 1e-07,
      tol.vectors = 1e-07,
      tol.solve = .Machine$double.eps,
      sparse = NULL,
      method = c("eigen", "Cholesky", "qr"),
      trace = FALSE,
      ...
    )

    dgl(x, med = 0, iqr = 1, chi = 0, xi = 0.6, maxit = 1000L)

    fitgl(
      x,
      start,
      inc = FALSE,
      na.rm = FALSE,
      method = c("mle", "hist", "prob", "quant", "shape"),
      ...
    )

    pgl(q, med = 0, iqr = 1, chi = 0, xi = 0.6, maxit = 1000L)

    qdgl(p, med = 0, iqr = 1, chi = 0, xi = 0.6)

    qgl(p, med = 0, iqr = 1, chi = 0, xi = 0.6)

    rgl(n, med = 0, iqr = 1, chi = 0, xi = 0.6)

### Value

Internal outputs

[Package EventPointer version 3.0.0 Index]