R/021.dynamic_imports.R

Defines functions .geometry .getPlatformDesign .cleanPlatformName `.sampleNames<-` .sampleNames `.featureNames<-` .featureNames `.protocolData<-` `.phenoData<-` `.assayData<-` .assayData `.annotation<-` .annotation .robustSmoothSpline .calibrateMultiscan .normalizeQuantileSpline .normalizeQuantile .normalizeFragmentLength .writeCdfQcUnits .writeCdfUnits .writeCdfHeader .writeCdf .readCcg .readCcgHeader .readPgfHeader .readPgfEnv .readCelRectangle .updateCelUnits .updateCel .convertCel .convertCdf .findCdf .cdfHeaderToCelHeader .compareCdfs .createCel .readCelUnits .readCel .readCelHeader .readCdfNbrOfCellsPerUnitGroup .readCdfIsPm .readCdfUnitNames .readCdfUnits .readCdfCellIndices .readCdfQc .readCdf .readCdfHeader .readCdfGroupNames .readBpmapHeader .readBpmap .cdfAddPlasqTypes .applyCdfGroups .invertMap

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Imports from affxparser
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
.invertMap <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::invertMap(...)
}

.applyCdfGroups <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::applyCdfGroups(...)
}

.cdfAddPlasqTypes <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::cdfAddPlasqTypes(...)
}

.readBpmap <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readBpmap(...)
}

.readBpmapHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readBpmapHeader(...)
}

.readCdfGroupNames <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfGroupNames(...)
}

.readCdfHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfHeader(...)
}

.readCdf <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdf(...)
}

.readCdfQc <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfQc(...)
}

.readCdfCellIndices <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfCellIndices(...)
}

.readCdfUnits <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfUnits(...)
}

.readCdfUnitNames <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfUnitNames(...)
}

.readCdfIsPm <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfIsPm(...)
}

.readCdfNbrOfCellsPerUnitGroup <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCdfNbrOfCellsPerUnitGroup(...)
}

.readCelHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCelHeader(...)
}

.readCel <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCel(...)
}

.readCelUnits <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCelUnits(...)
}

.createCel <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::createCel(...)
}

.compareCdfs <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::compareCdfs(...)
}

.cdfHeaderToCelHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::cdfHeaderToCelHeader(...)
}

.findCdf <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::findCdf(...)
}

.convertCdf <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::convertCdf(...)
}

.convertCel <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::convertCel(...)
}

.updateCel <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::updateCel(...)
}

.updateCelUnits <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::updateCelUnits(...)
}

.readCelRectangle <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCelRectangle(...)
}

.readPgfEnv <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readPgfEnv(...)
}

.readPgfHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readPgfHeader(...)
}

.readCcgHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCcgHeader(...)
}

.readCcg <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::readCcg(...)
}

.writeCdf <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::writeCdf(...)
}

.writeCdfHeader <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::writeCdfHeader(...)
}

.writeCdfUnits <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::writeCdfUnits(...)
}

.writeCdfQcUnits <- function(...) {
  requireNamespace("affxparser") || throw("Package not loaded: affxparser")
  affxparser::writeCdfQcUnits(...)
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Imports from aroma.light
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
.normalizeFragmentLength <- function(...) {
  requireNamespace("aroma.light") || throw("Package not loaded: aroma.light")
  aroma.light::normalizeFragmentLength(...)
}

.normalizeQuantile <- function(...) {
  requireNamespace("aroma.light") || throw("Package not loaded: aroma.light")
  aroma.light::normalizeQuantile(...)
}

.normalizeQuantileSpline <- function(...) {
  requireNamespace("aroma.light") || throw("Package not loaded: aroma.light")
  aroma.light::normalizeQuantileSpline(...)
}

.calibrateMultiscan <- function(...) {
  requireNamespace("aroma.light") || throw("Package not loaded: aroma.light")
  aroma.light::calibrateMultiscan(...)
}

.robustSmoothSpline <- function(...) {
  requireNamespace("aroma.light") || throw("Package not loaded: aroma.light")
  aroma.light::robustSmoothSpline(...)
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Imports for BiocGenerics
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
.annotation <- function(...) {
  requireNamespace("BiocGenerics") || throw("Package not loaded: BiocGenerics")
  BiocGenerics::annotation(...)
}

`.annotation<-` <- function(..., value) {
  requireNamespace("BiocGenerics") || throw("Package not loaded: BiocGenerics")
  ns <- getNamespace("BiocGenerics")
  get("annotation<-", mode="function", envir=ns)(..., value=value)
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Imports for Biobase
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
.assayData <- function(...) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  Biobase::assayData(...)
}

`.assayData<-` <- function(..., value) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  ns <- getNamespace("Biobase")
  get("assayData<-", mode="function", envir=ns)(..., value=value)
}

`.phenoData<-` <- function(..., value) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  ns <- getNamespace("Biobase")
  get("phenoData<-", mode="function", envir=ns)(..., value=value)
}

`.protocolData<-` <- function(..., value) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  ns <- getNamespace("Biobase")
  get("protocolData<-", mode="function", envir=ns)(..., value=value)
}

.featureNames <- function(...) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  Biobase::featureNames(...)
}

`.featureNames<-` <- function(..., value) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  ns <- getNamespace("Biobase")
  get("featureNames<-", mode="function", envir=ns)(..., value=value)
}

.sampleNames <- function(...) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  Biobase::sampleNames(...)
}

`.sampleNames<-` <- function(..., value) {
  requireNamespace("Biobase") || throw("Package not loaded: Biobase")
  ns <- getNamespace("Biobase")
  get("sampleNames<-", mode="function", envir=ns)(..., value=value)
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Imports for oligo
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
.cleanPlatformName <- function(...) {
  requireNamespace("oligo") || throw("Package not loaded: oligo")
  oligo::cleanPlatformName(...)
}

.getPlatformDesign <- function(...) {
  requireNamespace("oligo") || throw("Package not loaded: oligo")
  oligo::getPlatformDesign(...)
}

.geometry <- function(...) {
  requireNamespace("oligo") || throw("Package not loaded: oligo")
  oligo::geometry(...)
}

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aroma.affymetrix documentation built on May 29, 2024, 4:32 a.m.