xGRsep: Function to obtain separator index.

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

Function to obtain separator index.

Description

xGRsep is supposed to obtain separator index.

Usage

xGRsep(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

a vector for separator index

See Also

xGRsep

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]

# c) get separator index
vec_sep <- xGRsep(data)

## End(Not run)

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