InternalFunctions: EventPointer Internal Functions

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

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, method = "quant")

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)

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,
  ...
)

control_2(
  B,
  symmetric = TRUE,
  tol.values = 1e-07,
  tol.vectors = 1e-07,
  out.B = TRUE,
  method = c("eigen", "Cholesky")
)

is.sparse_2(X, sparselim = 0.9, camp = 0.05)

hyperGeometricApproach(ExS, nSel, P_value_PSI, significance, resPred, N)

poissonBinomialApproach(ExS, nSel, P_value_PSI, significance, resPred, N)

significanceFunction(P_value_PSI, cSel, nSel, significance)

hyperMatrixRes(cSel, nSel, ExS, P_value_PSI, significance, N)

GseaApproach(P_value_PSI, ExS, significance, resPred, PSI_table = NULL)

WilcoxonApproach(
  P_value_PSI,
  ExS,
  significance,
  resPred,
  PSI_table = NULL,
  nSel,
  N
)

Wilcoxon.z.matrix(
  ExprT,
  GeneGO,
  alternative = c("two.sided", "less", "greater"),
  mu = 0,
  paired = FALSE,
  exact = NULL,
  correct = TRUE,
  conf.int = FALSE,
  conf.level = 0.95
)

MatrixRes(cSel, nSel, ExS, P_value_PSI, significance, N, nmTopEv)

myphyper(p, m, n, k, lower.tail = TRUE, log.p = FALSE)

reclasify_intern(SG, mievento, pp1, pp2, ppref)

Value

Internal outputs

jpromeror/EventPointer documentation built on March 5, 2025, 1:31 p.m.