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

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

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)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: dnet
Loading required package: supraHex
Loading required package: hexbin
Loading required package: ggplot2
Start at 2019-08-21 15:59:34

Attempt to download from https://github.com/hfang-bristol/RDataCentre/blob/master/Portal/ImmunoBase.RData?raw=true (at 2019-08-21 15:59:35)
Attempt to download from http://galahad.well.ox.ac.uk/bigdata/ImmunoBase.RData (at 2019-08-21 15:59:36)
Attempt to download from http://galahad.well.ox.ac.uk/bigdata/ImmunoBase.RData (at 2019-08-21 15:59:37)
'ImmunoBase' CANNOT be loaded (at 2019-08-21 15:59:38)

End at 2019-08-21 15:59:38
Runtime in total is: 4 secs

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XGR documentation built on Jan. 8, 2020, 5:06 p.m.