gwasExplorer: gwasExplorer

In paul-shannon/gwasExplorer: gwasExplorer

gwasExplorer

Description

score non-coding variants in GWAS loci to elucidate function

Methods

Public methods

• gwasExplorer$new()

• gwasExplorer$getRegion()

• gwasExplorer$getLinkageTable()

• gwasExplorer$loadLinkageTable()

• gwasExplorer$getChromLocs()

• gwasExplorer$getEQTLSummary()

• gwasExplorer$getEqtlsForGene()

• gwasExplorer$trenaMultiScore()

• gwasExplorer$getExpressionMatrixCodes()

• gwasExplorer$getExpressionMatrix()

• gwasExplorer$runTrena()

• gwasExplorer$scoreBrokenMotifs()

• gwasExplorer$clone()

---

Method new()

Creates a new instance of this [R6][R6::R6Class] class.

Usage

gwasExplorer$new(
  targetGene,
  locusName,
  tagSnp,
  shoulder,
  tissueName,
  tbl.prespecifiedRegion = NA
)

Arguments

targetGene

character

locusName

haracter, from GWAS studies, often meta-analyses

tagSnp

character

shoulder

numeric number of bases up and downstream to consider in lookups

tissueName

character selects expression & variants

Returns

a new instance of gwasExplorer

---

Method getRegion()

the regulatory region being studied

Usage

gwasExplorer$getRegion()

Returns

data.frame

---

Method getLinkageTable()

from halporeg, a table with both hg19 and hg38 coordinates

Usage

gwasExplorer$getLinkageTable()

Returns

data.frame

---

Method loadLinkageTable()

from halporeg, a table with both hg19 and hg38 coordinates

Usage

gwasExplorer$loadLinkageTable(tagSnp)

Arguments

tagSnp

character

Returns

data.frame

---

Method getChromLocs()

hg19 and hg38 chromosomal locations

Usage

gwasExplorer$getChromLocs(geneSymbol)

Arguments

geneSymbol

character, a HUGO human gene symbol

Returns

data.frame

---

Method getEQTLSummary()

retrieve a summary of eQTL studies currently available from embl return data.frame

Usage

gwasExplorer$getEQTLSummary()

---

Method getEqtlsForGene()

from all available sources, a table with both hg19 and hg38 coordinates

Usage

gwasExplorer$getEqtlsForGene(eqtl.catalog.studyIDs, pval.threshold)

Arguments

eqtl.catalog.studyIDs

character vector,

pval.threshold

numeric retain only eQTLs as or more significant than this

Returns

data.frame

---

Method trenaMultiScore()

build tms model

Usage

gwasExplorer$trenaMultiScore(tissueName, tbl.fimo, tbl.oc)

Arguments

tissueName

character as used by GTEx

tbl.fimo

data.frame, typically a very large & low threshold set of fimo scores

tbl.oc

data.frame, open chromatin from, e.g., ATAC-seq, as tissue- and cell-type specific as possible

shoulder

numeric number of bytes up- and downstream from the largst transcript

Returns

data.frame

---

Method getExpressionMatrixCodes()

getExpressionMatrixCodes: short names (codes) and file paths

Usage

gwasExplorer$getExpressionMatrixCodes()

Returns

list

---

Method getExpressionMatrix()

getExpressionMatrix

Usage

gwasExplorer$getExpressionMatrix(code)

Arguments

code

character, a short descriptive name, resolves to a file path

Returns

data.frame

---

Method runTrena()

run trena

Usage

gwasExplorer$runTrena(tfs, mtx.rna, tbl.tms)

Arguments

tfs

character vector, one or more transcription factor gene symbols

mtx.rna

matrix, gene expression of many genes across many conditions or samples

tbl.tms

data.frame, tf binding sites, annotated and scored in many ways

Returns

data.frame

---

Method scoreBrokenMotifs()

score broken motifs

Usage

gwasExplorer$scoreBrokenMotifs(max.pvalue, tbl.eqtls)

Arguments

max.pvalue

numeric

tbl.eqtls

data.frame rsids used as input to motifbreakR

---

Method clone()

The objects of this class are cloneable with this method.

Usage

gwasExplorer$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  gwex <- gwasExplorer$new(targetGene="NDUFS2", locusName="ADAMTS4", tagSnp="rs4575098")

paul-shannon/gwasExplorer documentation built on July 16, 2022, 4:33 p.m.