ssvFetchBigwig {seqsetvis} | R Documentation |
ssvFetchBigwig.single
on each. Appends grouping variable to each
resulting data.table and uses rbindlist to efficiently combine results.ssvFetchBigwig
iteratively calls fetchWindowedBigwig.single
.
See ssvFetchBigwig.single
for more info.
ssvFetchBigwig(file_paths, qgr, unique_names = NULL, names_variable = "sample", win_size = 50, win_method = c("sample", "summary")[1], summary_FUN = stats::weighted.mean, anchor = c("left", "left_unstranded", "center", "center_unstranded")[3], return_data.table = FALSE, n_cores = getOption("mc.cores", 1))
file_paths |
character vector of file_paths to load from. Alternatively, file_paths can be a data.frame or data.table whose first column is a character vector of paths and additial columns will be used as metadata. |
qgr |
Set of GRanges to query. For valid results the width of each
interval should be identical and evenly divisible by |
unique_names |
names to use in final data.table to designate source bigwig. |
names_variable |
The column name where unique_names are stored. Default is 'sample' |
win_size |
The window size that evenly divides widths in |
win_method |
character. one of c("sample", "summary"). Determines
if |
summary_FUN |
function. only relevant if win_method is "summary".
passed to |
anchor |
character, one of c("center", "center_unstranded", "left", "left_unstranded") |
return_data.table |
logical. If TRUE the internal data.table is returned instead of GRanges. Default is FALSE. |
n_cores |
integer number of cores to use. Uses mc.cores option if not supplied. |
if qgr
contains the range chr1:1-100 and win_size
is
10, values from positions chr1 5,15,25...85, and 95 will be
retrieved from bw_file
A tidy formatted GRanges (or data.table if specified) containing fetched values.
if(Sys.info()['sysname'] != "Windows"){ library(GenomicRanges) bw_f = system.file("extdata/test_loading.bw", package = "seqsetvis", mustWork = TRUE) bw_files = c("a" = bw_f, "b" = bw_f) qgr = GRanges("chrTest", IRanges(1, 30)) bw_gr = ssvFetchBigwig(bw_files, qgr, win_size = 10) bw_gr2 = ssvFetchBigwig(as.list(bw_files), qgr, win_size = 10) bw_dt = ssvFetchBigwig(bw_files, qgr, win_size = 10, return_data.table = TRUE) }