gwaswloc-class {gwascat} | R Documentation

## Class `"gwaswloc"`

### 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 <stvjc@channing.harvard.edu>

### References

http://www.genome.gov/gwastudies/

### Examples

    showClass("gwaswloc")

[Package gwascat version 2.12.0 Index]