ssvFetchBigwig.single: Fetch values from a bigwig appropriate for heatmaps etc.
In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

ssvFetchBigwig.single

R Documentation

Fetch values from a bigwig appropriate for heatmaps etc.

Description

ssvFetchBigwig.single Gets 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

ssvFetchBigwig.single(
  bw_file,
  qgr,
  win_size = 50,
  win_method = c("sample", "summary")[1],
  summary_FUN = stats::weighted.mean,
  anchor = c("left", "left_unstranded", "center", "center_unstranded")[3],
  return_data.table = FALSE,
  force_skip_centerFix = FALSE
)

Arguments

`bw_file`	The character vector path to bigwig files to read from.
`qgr`	Set of GRanges to query. For valid results the width of each interval should be identical and evenly divisible by `win_size`.
`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`.
`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.
`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".