ssvFetchBigwig: Iterates a character vector (ideally named) and calls...

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Iterates a character vector (ideally named) and calls ssvFetchBigwig.single on each. Appends grouping variable to each resulting data.table and uses rbindlist to efficiently combine results.

Description

ssvFetchBigwig iteratively calls fetchWindowedBigwig.single. See ssvFetchBigwig.single for more info.

Usage

ssvFetchBigwig(
  file_paths,
  qgr,
  unique_names = NULL,
  names_variable = "sample",
  win_size = 50,
  win_method = c("sample", "summary")[1],
  summary_FUN = stats::weighted.mean,
  fragLens = "not_used",
  anchor = c("left", "left_unstranded", "center", "center_unstranded")[3],
  return_data.table = FALSE,
  n_cores = getOption("mc.cores", 1),
  n_region_splits = 1,
  force_skip_centerFix = FALSE
)

Arguments

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 win_size.
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 qgr.
win_method	character. one of c("sample", "summary"). Determines if viewGRangesWinSample_dt or viewGRangesWinSummary_dt is used to represent each region in qgr.
summary_FUN	function. only relevant if win_method is "summary". passed to viewGRangesWinSummary_dt.
fragLens	never used by ssvFetchBigwig. Ignore.
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.
n_region_splits	integer number of splits to apply to qgr. The query GRanges will be split into this many roughly equal parts for increased parallelization. Default is 1, no split.
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".

Details

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

Value

A tidy formatted GRanges (or data.table if specified) containing fetched values.

Examples

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)
}

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.