run_get_wis: Run get_wis function
In robbueck/wisard: Perform wighted interval scheduling on a Genomic Ranges object

Description Usage Arguments Details Value

View source: R/WIS_functions.R

Runs the get_wis function on a set of weighted intervals given as a GRangesList object by taking into account several parameters.

run_get_wis(
  granges_list,
  is_circular,
  overhang = 0,
  use_strand = T,
  frame_col = NULL,
  score_col = "score",
  score_f = function(x, y, n) x + y,
  max_f = function(x, y, n) x + y,
  overlap = 0
)

`granges_list`	A set of intervals as a GRangesList object. Requires a interval-score to maximize over as a column specified in `score_col`.
`is_circular`	Boolean, set TRUE if scale is circular.
`overhang`	A non-negative integer. A non-negative integer specifying for a linearized circular scale how much of the end is overlapping with the start. Ignored if is_circular is FALSE.
`use_strand`	Boolean, if TRUE, overlapping intervals on different strand are considered compatible.
`frame_col`	Optional, column in `granges_list` containing frame information. If set, overlapping intervals on different strand are considered compatible.
`score_col`	Name of a column in `granges_list` containing integers or floats to be used as a score to maximize over.
`score_f`	Function to update the score of a set each time an element is added. Passed to `score_funct` in get_wis, see there for detailed description.
`max_f`	Function to calculate a set-score to maximize over. Passed to `max_funct` in get_wis, see there for detailed description.
`overlap`	A non-negative integer. The allowed overlap between two intervals.

This function runs the get_wis function on a set of intervals and allows to distinguish between intervals on different stradns or frames. For each of these settings,get_wis is run seperately. For detailed description of the output, see get_wis.

A GRangesList object with intervals compatible according to the specified options.

robbueck/wisard documentation built on Jan. 25, 2022, 12:35 a.m.