gwaswloc-class: Class '"gwaswloc"'

In vjcitn/gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Description

A container for GRanges instances representing information in the NHGRI GWAS catalog.

Objects from the Class

Objects can be created by calls of the form new("gwaswloc", ...). Any GRanges instance can be supplied.

Slots

extractDate:

character set manually in .onAttach code to indicate date of retrieval of base table

seqnames:

Object of class "Rle" typically representing chromosome numbers of loci associated with specific traits

ranges:

Object of class "IRanges" genomic coordinates for locus

strand:

Object of class "Rle" identifier of chromosome strand

elementMetadata:

Object of class "DataFrame" general DataFrame-class instance providing attributes for the locus-trait association

seqinfo:

Object of class "Seqinfo"

metadata:

Object of class "list"

Extends

Class "GRanges", directly. Class "GenomicRanges", by class "GRanges", distance 2. Class "Vector", by class "GRanges", distance 3. Class "GenomicRanges_OR_missing", by class "GRanges", distance 3. Class "GenomicRanges_OR_GRangesList", by class "GRanges", distance 3. Class "Annotated", by class "GRanges", distance 4.

Methods

[

signature(x = "gwaswloc"): a character argument to the bracket will be assumed to be a dbSNP identifier for a SNP locus, and records corresponding to this SNP are extracted; numeric indexes are supported as for GRanges-class instances.

getRsids

signature(x = "gwaswloc"): extract all dbSNP identifiers as a character vector

getTraits

signature(x = "gwaswloc"): extract all traits (NHGRI term 'Disease/Trait') as a character vector

subsetByChromosome

signature(x = "gwaswloc"): select records by chromosome, a vector of chromosomes may be supplied

subsetByTraits

signature(x = "gwaswloc"): select all records corresponding to a given vector of traits

Note

In gwascat package 1.9.6 and earlier, the globally accessible gwaswloc instance gwrngs was created upon attachment. This is no longer the case.

Author(s)

VJ Carey <[e-mail]>

References

http://www.ebi.ac.uk/gwas/

Examples

showClass("gwaswloc")

vjcitn/gwascat documentation built on May 5, 2019, 7:59 p.m.