EndophenotypeExplorer-class: EndophenotypeExplorer

In PriceLab/endophenotypeExplorer: EndophenotypeExplorer

EndophenotypeExplorer

Description

R6 Class for exploring associations between eQTLs, variants, gene expression and gene regulation

An endophenotypeExplore has access to eQTLs, variant calls, and more

Value

the url

Methods

Public methods

• EndophenotypeExplorer$new()

• EndophenotypeExplorer$setTargetGene()

• EndophenotypeExplorer$setTargetChromosome()

• EndophenotypeExplorer$get.rna.matrix.codes()

• EndophenotypeExplorer$get.rna.matrix()

• EndophenotypeExplorer$setupVcfURL()

• EndophenotypeExplorer$getVcfUrl()

• EndophenotypeExplorer$getGenoMatrix()

• EndophenotypeExplorer$getGenoMatrixByRSID()

• EndophenotypeExplorer$get.ampad.EQTLsForGene()

• EndophenotypeExplorer$getEQTLsInRegion()

• EndophenotypeExplorer$getIdMap()

• EndophenotypeExplorer$biomart.rsidToLoc()

• EndophenotypeExplorer$rsidToLoc()

• EndophenotypeExplorer$new.rsidToLoc()

• EndophenotypeExplorer$biomart.locsToRSID()

• EndophenotypeExplorer$locsToRSID()

• EndophenotypeExplorer$mapSampleIdToPatientAndCohort()

• EndophenotypeExplorer$setupClinicalData()

• EndophenotypeExplorer$getClinicalTable()

• EndophenotypeExplorer$setupGWASData()

• EndophenotypeExplorer$getGWASTables()

• EndophenotypeExplorer$identifyTargetGeneChromosome()

• EndophenotypeExplorer$get.rosmap.patient.table()

• EndophenotypeExplorer$get.sinai.patient.table()

• EndophenotypeExplorer$get.mayo.patient.table()

• EndophenotypeExplorer$sampleID.to.clinicalTable()

• EndophenotypeExplorer$getStandardClinicalColumnNames()

• EndophenotypeExplorer$standardizeMayoPatientTable()

• EndophenotypeExplorer$standardizeRosmapPatientTable()

• EndophenotypeExplorer$standardizeSinaiPatientTable()

• EndophenotypeExplorer$getAggregatedAlleleFrequencies()

• EndophenotypeExplorer$getTissueExpression()

• EndophenotypeExplorer$splitExpressionMatrixByMutationStatusAtRSID()

• EndophenotypeExplorer$splitMayoRnaMatrixByGenotype()

• EndophenotypeExplorer$splitSinaiRnaMatrixByGenotype()

• EndophenotypeExplorer$splitRosmapRnaMatrixByGenotype()

• EndophenotypeExplorer$trenaScoreGenotypeStratifiedExpression()

• EndophenotypeExplorer$subsetAndRelabelGenoMatrixByPatientIDs()

• EndophenotypeExplorer$extremeBraakScoreSignificanceAtRSID()

• EndophenotypeExplorer$clone()

---

Method new()

Create a new EndophenotypeExplorer object

Usage

EndophenotypeExplorer$new(
  target.gene,
  default.genome,
  vcf.project,
  chromosome = NA,
  verbose = FALSE,
  initialize.snpLocs = FALSE,
  defer.setupClinicalData.toSupportTesting = FALSE
)

Arguments

target.gene

Gene of interest.

default.genome

UCSC code, either 'hg19' or 'hg38'.

vcf.project

character, either "ADNI" or "AMPAD"

chromosome

default NA, may be unusual cases where we supply it (C2orf90/ECRG4) for instance

verbose

logical

initialize.snpLocs

logical, force this ~60 second process at startup

Returns

A new 'EndophenotypeExplorer' object.

---

Method setTargetGene()

the targetGene and genome are widely referenced - this member function allows you to change your initial choices

Usage

EndophenotypeExplorer$setTargetGene(targetGene, genome, chromosome = NA)

Arguments

genome

UCSC code, either 'hg19' or 'hg38'.

chromosome

default NA, causing a lookup

target.gene

Gene of interest.

---

Method setTargetChromosome()

the target chromosome and genome are widely referenced - this member function allows you to change your initial choices

Usage

EndophenotypeExplorer$setTargetChromosome(target.chromosome, genome)

Arguments

genome

UCSC code, either 'hg19' or 'hg38'.

---

Method get.rna.matrix.codes()

Usage

EndophenotypeExplorer$get.rna.matrix.codes()

---

Method get.rna.matrix()

Usage

EndophenotypeExplorer$get.rna.matrix(code)

---

Method setupVcfURL()

our genotypes are stored per-chromosome in vcf files. this function uses the current chromosome of interest, to provide otherwise simple access to genotypes of the current gene and its putative regulatory regions

Usage

EndophenotypeExplorer$setupVcfURL(chromosome)

---

Method getVcfUrl()

easy access to the current value returns url in character form

Usage

EndophenotypeExplorer$getVcfUrl()

---

Method getGenoMatrix()

genotypes for all samples in the specified locus

Usage

EndophenotypeExplorer$getGenoMatrix(chrom, start, end)

Arguments

chrom

character

start

numeric

end

numeric returns matrix, location by sample

---

Method getGenoMatrixByRSID()

genotypes for all samples at the specified rsids

Usage

EndophenotypeExplorer$getGenoMatrixByRSID(rsids)

Arguments

rsids

character returns matrix, location by sample

---

Method get.ampad.EQTLsForGene()

Usage

EndophenotypeExplorer$get.ampad.EQTLsForGene()

---

Method getEQTLsInRegion()

Usage

EndophenotypeExplorer$getEQTLsInRegion(chrom, start, end)

---

Method getIdMap()

Usage

EndophenotypeExplorer$getIdMap()

---

Method biomart.rsidToLoc()

Usage

EndophenotypeExplorer$biomart.rsidToLoc(rsids)

---

Method rsidToLoc()

Usage

EndophenotypeExplorer$rsidToLoc(rsids)

---

Method new.rsidToLoc()

Usage

EndophenotypeExplorer$new.rsidToLoc(rsids)

---

Method biomart.locsToRSID()

Usage

EndophenotypeExplorer$biomart.locsToRSID(locs, genome)

---

Method locsToRSID()

Usage

EndophenotypeExplorer$locsToRSID(locs, genome)

---

Method mapSampleIdToPatientAndCohort()

Usage

EndophenotypeExplorer$mapSampleIdToPatientAndCohort(sampleID)

---

Method setupClinicalData()

Usage

EndophenotypeExplorer$setupClinicalData()

---

Method getClinicalTable()

Usage

EndophenotypeExplorer$getClinicalTable()

---

Method setupGWASData()

Usage

EndophenotypeExplorer$setupGWASData()

---

Method getGWASTables()

Usage

EndophenotypeExplorer$getGWASTables()

---

Method identifyTargetGeneChromosome()

Usage

EndophenotypeExplorer$identifyTargetGeneChromosome(target.gene)

---

Method get.rosmap.patient.table()

Usage

EndophenotypeExplorer$get.rosmap.patient.table(patientID)

---

Method get.sinai.patient.table()

Usage

EndophenotypeExplorer$get.sinai.patient.table(patientID)

---

Method get.mayo.patient.table()

Usage

EndophenotypeExplorer$get.mayo.patient.table(patientID)

---

Method sampleID.to.clinicalTable()

Usage

EndophenotypeExplorer$sampleID.to.clinicalTable(sampleID)

---

Method getStandardClinicalColumnNames()

Usage

EndophenotypeExplorer$getStandardClinicalColumnNames()

---

Method standardizeMayoPatientTable()

Usage

EndophenotypeExplorer$standardizeMayoPatientTable(tbl)

---

Method standardizeRosmapPatientTable()

Usage

EndophenotypeExplorer$standardizeRosmapPatientTable(tbl)

---

Method standardizeSinaiPatientTable()

Usage

EndophenotypeExplorer$standardizeSinaiPatientTable(tbl)

---

Method getAggregatedAlleleFrequencies()

Usage

EndophenotypeExplorer$getAggregatedAlleleFrequencies(rsid, quiet = TRUE)

---

Method getTissueExpression()

Usage

EndophenotypeExplorer$getTissueExpression(geneSymbol, tissue)

---

Method splitExpressionMatrixByMutationStatusAtRSID()

Usage

EndophenotypeExplorer$splitExpressionMatrixByMutationStatusAtRSID(
  mtx,
  rsid,
  study.name
)

---

Method splitMayoRnaMatrixByGenotype()

Usage

EndophenotypeExplorer$splitMayoRnaMatrixByGenotype(mtx, rsid)

---

Method splitSinaiRnaMatrixByGenotype()

Usage

EndophenotypeExplorer$splitSinaiRnaMatrixByGenotype(mtx, rsid)

---

Method splitRosmapRnaMatrixByGenotype()

Usage

EndophenotypeExplorer$splitRosmapRnaMatrixByGenotype(mtx, rsid)

---

Method trenaScoreGenotypeStratifiedExpression()

Usage

EndophenotypeExplorer$trenaScoreGenotypeStratifiedExpression(
  mtx.1,
  mtx.2,
  targetGene,
  tfs
)

---

Method subsetAndRelabelGenoMatrixByPatientIDs()

Usage

EndophenotypeExplorer$subsetAndRelabelGenoMatrixByPatientIDs(
  mtx.geno,
  studyName
)

---

Method extremeBraakScoreSignificanceAtRSID()

Usage

EndophenotypeExplorer$extremeBraakScoreSignificanceAtRSID(rsid)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

EndophenotypeExplorer$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

PriceLab/endophenotypeExplorer documentation built on Sept. 14, 2022, 5:14 p.m.