GwasLocusScores: GwasLocusScores

In paul-shannon/gwasLocusScores: GwasLocusScores

GwasLocusScores

Description

assess RNA-binding protein binding sites, their structure and motif matches

Value

nothing

a data.frame

a data.frame

a data.frame

a data.frame

Public fields

rbp

the gene symbol name of the protein

Active bindings

rbp

the gene symbol name of the protein

Methods

Public methods

• GwasLocusScores$new()

• GwasLocusScores$set.eqtls()

• GwasLocusScores$get.tbl.eqtl()

• GwasLocusScores$breakMotifsAtEQTLs()

• GwasLocusScores$createTrenaMultiScoreTable()

• GwasLocusScores$runTrena()

• GwasLocusScores$getADVX()

• GwasLocusScores$getETX()

• GwasLocusScores$scoreEQTLs()

• GwasLocusScores$clone()

---

Method new()

Creates a new instance of this class.

Usage

GwasLocusScores$new(tag.snp, chrom, start.loc, end.loc, targetGene)

Arguments

tag.snp

character, an rsid identifying the locus

chrom

character, e.g., "chr1"

start.loc

numeric the start of the genomic region of interest

end.loc

numeric the end of the genomic region of interest

targetGene

character, e.g. "NDUFS2"

Returns

an object of the GwasLocusScores class

---

Method set.eqtls()

specifies the eqtls to be used

Usage

GwasLocusScores$set.eqtls(tbl.eqtls)

---

Method get.tbl.eqtl()

extract all previously obtained eQTLs at or above the specified pvalue threshold

Usage

GwasLocusScores$get.tbl.eqtl(pvalue.cutoff)

Arguments

pvalue.cutoff

numeric, e.g., 1e-4

---

Method breakMotifsAtEQTLs()

discover which motifs are broken by the eQTL variants, for specified gene and pval

Usage

GwasLocusScores$breakMotifsAtEQTLs(
  targetGene,
  pvalue.cutoff = NA,
  TFs.preselected = NA
)

Arguments

targetGene

character, a gene symbol in the eQTL table

pvalue.cutoff

numeric, e.g., 1e-4

TFs.preselected

character, e.g., c("SOX21", "ZEB1")

---

Method createTrenaMultiScoreTable()

use FIMO and open chromatin, and TrenaMultiScore capabilities to create a tbl.tms

Usage

GwasLocusScores$createTrenaMultiScoreTable(
  trenaProject,
  tbl.fimo,
  tbl.oc,
  mtx.rna = NA
)

Arguments

trenaProject

a concrete TrenaProject object, e.g., TrenaProjectAD()

tbl.fimo

data.frame

tbl.oc

data.frame

mtx.rna

matrix

---

Method runTrena()

given tfs, implicit target gene and an expression matrix, run trena

Usage

GwasLocusScores$runTrena(tfs, mtx.rna, tbl.tms.final = NA)

Arguments

tfs

character, a vector of transcription factor geneSymbol names

mtx.rna

matrix

tbl.tms.final

data.frame, a TrenaMultiScore table from which the tfs came

---

Method getADVX()

access to the ADvariantExplorer object

Usage

GwasLocusScores$getADVX()

---

Method getETX()

access to the EndophenotypeExplorer object

Usage

GwasLocusScores$getETX()

---

Method scoreEQTLs()

calculates the aggregate impact of broken motifs for TFs in the trena model

Usage

GwasLocusScores$scoreEQTLs(tbl.trena, tbl.breaks, tbl.eqtl)

Arguments

tbl.trena

data.frame

tbl.breaks

data.frame from motifbreakR

tbl.eqtl

data.frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

GwasLocusScores$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  gls <- GwasLocusScores("rs4575096")

paul-shannon/gwasLocusScores documentation built on April 5, 2022, 6:30 a.m.