R/xGRsort.r

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

#' Function to sort by chromosomes/seqnames, start and end coordinates of the intervals.
#'
#' \code{xGRsort} is supposed to sort by chromosomes/seqnames, start and end coordinates of the intervals. 
#'
#' @param 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'
#' @return index
#' @export
#' @seealso \code{\link{xGR}}
#' @include xGRsort.r
#' @examples
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
#' \dontrun{
#'
#' # 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]
#' }

xGRsort <- function(data)
{
	data <- gsub(',.*','',data)
	
	## have to be formatted as chr:start-end
    input <- do.call(rbind, strsplit(data, ":|-|,"))
    if(ncol(input)==2) {
     	data <- paste(input[,1], ":", input[,2], "-", input[,2], sep="")
    }
	##
	
	## gr has unique regions
	suppressWarnings(gr <- xGR(data, format='chr:start-end'))
	
	## just in case input is not 'chr:start-end' (for example, region names)
	if(is.null(gr)){
		return(NULL)
	}
	
	gr <- GenomeInfoDb::sortSeqlevels(gr)
	
	gr <- sort(gr)
	
	############################
	## very important (because of non-redundant)
	df <- data.frame(sid=1:length(gr), gr=names(gr), stringsAsFactors=FALSE)
	ind <- match(data, df$gr)
	df <- df[ind, ]
	df$oid <- 1:length(data)
	sid <- NULL
	df <- df %>% dplyr::arrange(sid)
	############################
	
  	invisible(df$oid)

}