xGRsort: Function to sort by chromosomes/seqnames, start and end...

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

Description

xGRsort is supposed to sort by chromosomes/seqnames, start and end coordinates of the intervals.

Usage

xGRsort(data)

Arguments

data	input genomic regions (GR). GR should be provided as a vector in the format of 'chrN:start-end', where N is either 1-22 or X, start (or end) is genomic positional number; for example, 'chr1:13-20'

Value

index

See Also

xGRsort

Examples

## Not run: 
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

# a) provide the genomic regions
## load ImmunoBase
ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
RData.location=RData.location)
## get lead SNPs reported in AS GWAS and their significance info (p-values)
gr <- ImmunoBase$AS$variant
cse <- xGRcse(gr)

# b) sort index
ind <- xGRsort(cse)
data <- cse[ind]

## End(Not run)

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