get_count_matrix {ODER} | R Documentation |
Scores the mean coverage of the expressed regions as a count matrix
get_count_matrix(bw_paths, annot_ers, cols = NULL)
bw_paths |
Vector containing the bigwig file paths to read in |
annot_ers |
GRangesList containing the annotated ERs
(product of |
cols |
A dataframe containing the information to be used as colData for the output. If NULL then the bw_paths will be used for the colData |
A Ranged Summarized Experiment containing the gene counts as an assay
megadepth::install_megadepth() rec_url <- recount::download_study( project = "SRP012682", type = "samples", download = FALSE ) # file_cache is an internal function to download a bigwig file from a link # if the file has been downloaded recently, it will be retrieved from a cache bw_path <- file_cache(rec_url[1]) ex_opt_ers <- GenomicRanges::GRanges( seqnames = S4Vectors::Rle(c("chr1", "chr2"), c(4, 1)), ranges = IRanges::IRanges( start = c(1:5), end = seq(100, 500, 100) ) ) example_cm <- get_count_matrix( bw_paths = c(bw_path, bw_path), annot_ers = ex_opt_ers ) example_cm