InternalFunctions {EventPointer} | R Documentation |
Internal functions used by EventPointer in the different steps of the algorithm
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)
Internal outputs