ssvFetchGRanges: Fetch coverage values for a list of GRanges.

Description Usage Arguments Value Examples

View source: R/functions_fetch_GRanges.R

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

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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

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seqsetvis documentation built on Nov. 8, 2020, 5:57 p.m.