get_ers {ODER} | R Documentation |
get_ers
defines expressed regions across an inputted range of mean
coverage cut-offs (MCCs) and max region gaps (MRGs) from the coverage.
get_strand_ers
defines ERs across an inputted range of mean coverage
cut-offs (MCCs) and max region gaps (MRGs) from the coverage.
get_ers(coverage, mccs, mrgs) get_strand_ers( bw_pos, bw_neg, auc_raw_pos, auc_raw_neg, auc_target, chrs, mccs, mrgs, bw_chr = "chr" )
coverage |
the coverage of the bigwig files passed into
|
mccs |
mean coverage cut-offs to apply. |
mrgs |
max region gaps to apply. |
bw_pos |
positive strand bigwig file |
bw_neg |
negative strand bigwig file |
auc_raw_pos |
vector containing AUCs(Area Under Coverage) matching the order of the positive bigwig paths. |
auc_raw_neg |
vector containing AUCs(Area Under Coverage) matching the order of the negative bigwig paths. |
auc_target |
total AUC to normalise all samples to. E.g. 40e6 * 100 would be the estimated total auc for sample sequenced to 40 million reads of 100bp in length. |
chrs |
chromosomes to obtain mean coverage for, default is "" giving every chromosome. Can take UCSC format(chrs = "chr1") or just the chromosome i.e. chrs = c(1,X) |
bw_chr |
specifies whether the bigwig files has the chromosomes labelled with a "chr" preceding the chromosome i.e. "chr1" vs "1". Can be either "chr" or "nochr" with "chr" being the default. |
list containing sets of ERs, each generated using a particular combination of MCC and MRG.
list containing sets of stranded ERs, each generated using a particular combination of MCC and MRG.
get_strand_ers
: Method for getting ers from stranded BigWig files
data(gtex_SRP012682_SRX222703_lung_coverage_1, package = "ODER") eg_ers <- get_ers( coverage = gtex_SRP012682_SRX222703_lung_coverage_1, mccs = c(5, 10), mrgs = c(10, 20) ) eg_ers library("magrittr") gtex_metadata <- recount::all_metadata("gtex") gtex_metadata <- gtex_metadata %>% as.data.frame() %>% dplyr::filter(project == "SRP012682") 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_plus <- file_cache(rec_url[58]) bw_minus <- file_cache(rec_url[84]) # As of rtracklayer 1.25.16, BigWig is not supported on Windows. if (!xfun::is_windows()) { stranded_ers <- get_strand_ers( bw_pos = bw_plus, bw_neg = bw_minus, auc_raw_pos = gtex_metadata[["auc"]][58], auc_raw_neg = gtex_metadata[["auc"]][84], auc_target = 40e6 * 100, chrs = "chr21", mccs = c(5, 10), mrgs = c(10, 20) ) stranded_ers }