R/convert_sumstats.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Convert summary statistics to desired object type
#'
#' @return Summary statistics in the converted format
#'
#' @inheritParams format_sumstats
#' @param return_format Object type to convert to;
#'  \code{"data.table"}, \code{"GenomicRanges"} or
#'  \code{"VRanges"}(default is \code{"data.table"}).
#' @keywords internal
convert_sumstats <- function(sumstats_dt,
                             return_format = c("data.table", 
                                               "vranges", 
                                               "granges")) {
    return_format <- return_format[1]
    if (tolower(return_format) %in% c("vr", "vranges")) {
        out <- to_vranges(sumstats_dt = sumstats_dt)
        return(out)
    } else if (tolower(return_format) %in% c("gr",
                                             "granges",
                                             "genomicranges")) {
        out <- to_granges(sumstats_dt = sumstats_dt)
        return(out)
    } else {
        return(sumstats_dt)
    }
}