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") 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)
Internal outputs