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

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

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

xGR

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 

# 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)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.