ADvariantExplorer: ADvariantExplorer

In paul-shannon/ADvariantExplorer: ADvariantExplorer

ADvariantExplorer

Description

access to GWAS and eQTL data, slighly optimized for Alzheimer's disease

Methods

Public methods

• ADvariantExplorer$new()

• ADvariantExplorer$getTargetGene()

• ADvariantExplorer$getFilteredGwasTable()

• ADvariantExplorer$getFullGwasTable()

• ADvariantExplorer$geteQTLSummary()

• ADvariantExplorer$geteqtlStudyNamesForGroup()

• ADvariantExplorer$geteQTLsByLocationAndStudyID()

• ADvariantExplorer$getCellTypes()

• ADvariantExplorer$clone()

---

Method new()

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

Usage

ADvariantExplorer$new(targetGene, loc.chrom, loc.start, loc.end)

Arguments

targetGene

character, a candidate gene for this AD GWAS locus

loc.chrom

character, the chromosome of the region to consider

loc.start

numeric, the start of the region to consider

loc.end

numeric, the end of the region to consider

Returns

a new instance of ADvariantExplorer

---

Method getTargetGene()

accessor for the object's targetGene field

Usage

ADvariantExplorer$getTargetGene()

Returns

the current value of the targetGene member

---

Method getFilteredGwasTable()

access to the EMBL-EBI GWAS catalog via bioc, filtered by location and/or targetGene

Usage

ADvariantExplorer$getFilteredGwasTable(
  targetGeneOnly = TRUE,
  studyString = "alzheimer",
  trim.columns = TRUE
)

Arguments

targetGeneOnly

logical, default TRUE, otherwise all variants in this regeion,

studyString

character, default "alzheimer", possibly empty string or any other study field matchabel substring affecting any gene whatsoever

Returns

a data.frame

---

Method getFullGwasTable()

access to the complete EMBL-EBI GWAS catalog via bioc

Usage

ADvariantExplorer$getFullGwasTable(trim.columns = FALSE)

Arguments

trim.columns

logical reduce to a legible 7 columns

Returns

a data.frame

---

Method geteQTLSummary()

access to the complete EMBL-EBI eQTL Catalogue via the catalogueR R package, focusing on expression cis-QTLs and sQTL (splicing)

Usage

ADvariantExplorer$geteQTLSummary()

Returns

a data.frame

---

Method geteqtlStudyNamesForGroup()

returns the retrieval-ready study names given

Usage

ADvariantExplorer$geteqtlStudyNamesForGroup(groupMatchingString)

Arguments

groupMatchingString

character, (part of) a qtl_group string

Returns

a data.frame

---

Method geteQTLsByLocationAndStudyID()

access to the complete EMBL-EBI eQTL Catalogue via the catalogueR R package, focusing on expression cis-QTLs and sQTL (splicing

Usage

ADvariantExplorer$geteQTLsByLocationAndStudyID(
  chrom,
  start,
  end,
  studyIDs,
  targetGene.only = TRUE,
  simplify = FALSE
)

Arguments

chrom

character

start

numeric

end

numeric

studyIDs

character vector, one or more values from eQTL summary unique_id column

targetGene.only

logical, default TRUE, otherwise result has all eQTL genes in the region

simplify

logical, trims columns to just the crucial 4: rsid, pvalue, gene, samples

method

character, either REST or tabix, REST by default

Returns

a data.frame ordered by increasing pvalue.QTL

---

Method getCellTypes()

returns one gene's cell types, or the entire table from jiang et al 2020, nine cell types across 10 human (and mouse) brain regions: https://www.sciencedirect.com/science/article/pii/S2589004220309664 scREAD: A Single-Cell RNA-Seq Database for Alzheimer's Disease

Usage

ADvariantExplorer$getCellTypes(geneSymbol = NA)

Arguments

geneSymbol

character string, either a HUGO gene symbol, or NA

Returns

a character vector or a data.frame (if geneSymbol param is NA)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ADvariantExplorer$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

paul-shannon/ADvariantExplorer documentation built on May 13, 2022, 5:07 a.m.