ssvFetchGRanges {seqsetvis} | R Documentation

## 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

    ssvFetchGRanges(CTCF_in_10a_narrowPeak_grs, CTCF_in_10a_overlaps_gr, win_size = 200)

[Package seqsetvis version 1.7.5 Index]