R/example_bg_bw.R

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

#' Example bedGraph/bigWig files
#' 
#' Download examples bedGraph and bigWig files.
#' @inheritParams get_geo_links
#' @inheritParams GenomicRanges::GRanges
#' @returns Named list of file paths.
#' 
#' @export
#' @importFrom GenomicRanges GRanges
#' @importFrom rtracklayer import export.bedGraph export.bw
#' @examples 
#' files <- example_bg_bw()
example_bg_bw <- function(gsm="GSM4703766",
                          ranges = "chr6:165169213-167169213"){
    
    links <- get_geo_links(gsm = gsm) 
    query_granges <- GenomicRanges::GRanges(ranges)
    gr <- rtracklayer::import(con = links$bedgraph,
                              which = query_granges)
    gr <- fix_seqinfo(gr = gr, build = "hg19")
    #### save ####
    bg <- tempfile(fileext = ".bedgraph")
    rtracklayer::export.bedGraph(object = gr, con = bg)
    bw <- tempfile(fileext = ".bigwig") 
    
    rtracklayer::export.bw(object = gr, con = bw)
    return(list(gr=gr,
                bedgraph=bg,
                bigwig=bw))
}