ssvFetchGRanges: Fetch coverage values for a list of GRanges.

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

Fetch coverage values for a list of GRanges.

Description

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.

Usage

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
)

Arguments

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".

Value

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

Examples

data(CTCF_in_10a_narrowPeak_grs)
data(CTCF_in_10a_overlaps_gr)
ssvFetchGRanges(CTCF_in_10a_narrowPeak_grs, CTCF_in_10a_overlaps_gr, win_size = 200)

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