InternalFunctions: EventPointer Internal Functions

In EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq data

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

EventPointer documentation built on Nov. 8, 2020, 7:12 p.m.