ImmunoBase: Immune-disease associated variants, regions and genes from...

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Immune-disease associated variants, regions and genes from ImmunoBase (hg19)

Description

This dataset contains data obtained from ImmunoBase. For each of 20 immune-diseases, its associated variants, regions, and nearby genes (within 500kb) are stored.

Usage

data(ImmunoBase)

Value

a list with 5 components:

• disease: a character of disease name

• variants: an object of class "GRanges", storing genomic locations of associated variants plus their significance and odd ratios

• regions: an object of class "GRanges", storing genomic locations of associated regions

• genes_variants: a named vector for nearby genes within 500kb of associated variants; the element names are gene symbols, the element values for the shortest distance to all associated variants

• genes_regions: a named vector for nearby genes within 500kb of associated regions; the element names are gene symbols, the element values for the shortest distance to all associated regions

Examples

## Not run: 
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase')
names(ImmunoBase)
ImmunoBase$AS$disease
ImmunoBase$AS$variants
head(ImmunoBase$AS$genes_variants)
head(ImmunoBase$AS$genes_regions)

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.