ssvFetchGRanges: Fetch coverage values for a list of GRanges.
In seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Description Usage Arguments Value Examples

View source: R/functions_fetch_GRanges.R

ssvFetchGRanges Gets coverage values for each region of the query GRanges (qgr). Values correspond to the center of each window of size win_size. A tidy formatted data.table object is returned suitable for plotting using ggplots.

ssvFetchGRanges(
  grs,
  qgr,
  file_attribs = data.frame(matrix(0, nrow = length(grs), ncol = 0)),
  unique_names = names(grs),
  names_variable = "sample",
  win_size = 50,
  win_method = c("sample", "summary")[1],
  summary_FUN = function(x, w) max(x),
  target_strand = c("*", "+", "-", "both")[1],
  use_coverage = NULL,
  attrib_var = "score",
  fill_value = 0,
  anchor = c("left", "left_unstranded", "center", "center_unstranded")[3],
  return_data.table = FALSE,
  n_cores = getOption("mc.cores", 1),
  force_skip_centerFix = FALSE
)

`grs`	a list of GRanges for which to calculate coverage.
`qgr`	Set of GRanges to query. For valid results the width of each interval should be identical and evenly divisible by `win_size`.
`file_attribs`	data.frame (1 row per item in grs) containing attributes to append to results.
`unique_names`	The column name where unique_names are stored. Default is 'sample'
`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`.
`target_strand`	character. if one of "+" or "-", reads are filtered to match. ignored if any other value.
`use_coverage`	boolean or NULL, if TRUE, query regions are scored by the number of intervals overlapping. Default of NULL checks if attrib_var is "score" and uses coverage if so.
`attrib_var`	character, column in mcols of GRanges to pull values from. Default of "score" is compatible with internal coverage calculation or bedgraph-like files.
`fill_value`	numeric or character value to use where queried regions are empty. Default is 0 and appropriate for both calculated coverage and bedgraph/bigwig like files. Will automatically switch to "MISSING" if data is guessed to be qualitative.
`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.
`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".