| ssvFetchSignal {seqsetvis} | R Documentation |
Does nothing unless load_signal is overridden to carry out reading
data from file_paths (likely via the appropriate ssvFetch* function,
ie. ssvFetchBigwig or ssvFetchBam
ssvFetchSignal(
file_paths,
qgr,
unique_names = NULL,
names_variable = "sample",
win_size = 50,
win_method = c("sample", "summary")[1],
return_data.table = FALSE,
load_signal = function(f, nam, qgr) { warning("nothing happened, ",
"supply a function to", "load_signal parameter.") },
n_cores = getOption("mc.cores", 1),
force_skip_centerFix = FALSE
)
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 |
GRanges of intervals to return from each file |
unique_names |
unique file ids for each file in file_paths. Default is names of file_paths vector |
names_variable |
character, variable name for column containing unique_names entries. Default is "sample" |
win_size |
numeric/integer window size resolution to load signal at. Default is 50. |
win_method |
character. one of c("sample", "summary"). Determines
if |
return_data.table |
logical. If TRUE data.table is returned instead of GRanges, the default. |
load_signal |
function taking f, nam, and qgr arguments. f is from file_paths, nam is from unique_names, and qgr is qgr. See details. |
n_cores |
integer number of cores to use. Uses mc.cores option if not supplied. |
force_skip_centerFix |
boolean, if TRUE all query ranges will be used "as is". This is already the case by default if win_method == "summary" but may have applications where win_method == "sample". |
load_signal is passed f, nam, and qgr and is executed in the
environment where load_signal is defined. See
ssvFetchBigwig and ssvFetchBam
for examples.
A GRanges with values read from file_paths at intervals of win_size. Originating file is coded by unique_names and assigned to column of name names_variable. Output is data.table is return_data.table is TRUE.
library(GenomicRanges)
bam_f = system.file("extdata/test.bam",
package = "seqsetvis", mustWork = TRUE)
bam_files = c("a" = bam_f, "b" = bam_f)
qgr = CTCF_in_10a_overlaps_gr[1:2]
qgr = resize(qgr, 500, "center")
load_bam = function(f, nam, qgr) {
message("loading ", f, " ...")
dt = seqsetvis:::ssvFetchBam.single(bam_f = f,
qgr = qgr,
win_size = 50,
fragLen = NULL,
target_strand = "*",
return_data.table = TRUE)
dt[["sample"]] = nam
message("finished loading ", nam, ".")
dt
}
ssvFetchSignal(bam_files, qgr, load_signal = load_bam)