ssvFetchBigwig.single {seqsetvis} | 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".

### 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 GRanges (or data.table if specified) containing fetched values.

[Package seqsetvis version 1.14.4 Index]