gbins.summary: Calculates summary statistics of a track expression for bins

In misha: Toolkit for Analysis of Genomic Data

Calculates summary statistics of a track expression for bins

Description

Calculates summary statistics of a track expression for bins.

Usage

gbins.summary(
  ...,
  expr = NULL,
  intervals = get("ALLGENOME", envir = .misha),
  include.lowest = FALSE,
  iterator = NULL,
  band = NULL
)

Arguments

...	pairs of track expressions ('bin_expr') that determines the bins and breaks that define the bins. See gdist.
expr	track expression for which summary statistics is calculated
intervals	genomic scope for which the function is applied
include.lowest	if 'TRUE', the lowest value of the range determined by breaks is included
iterator	track expression iterator. If 'NULL' iterator is determined implicitly based on track expressions.
band	track expression band. If 'NULL' no band is used.

Details

This function is a binned version of 'gsummary'. For each iterator interval the value of 'bin_expr' is calculated and assigned to the corresponding bin determined by 'breaks'. The summary statistics of 'expr' are calculated then separately for each bin.

The bins can be multi-dimensional depending on the number of 'bin_expr'-'breaks' pairs.

The range of bins is determined by 'breaks' argument. For example: 'breaks=c(x1, x2, x3, x4)' represents three different intervals (bins): (x1, x2], (x2, x3], (x3, x4].

If 'include.lowest' is 'TRUE' the the lowest value will be included in the first interval, i.e. in [x1, x2].

Value

Multi-dimensional array representing summary statistics for each bin.

See Also

gsummary, gintervals.summary, gdist

Examples

gdb.init_examples()
gbins.summary("dense_track", c(0, 0.2, 0.4, 2), "sparse_track",
    intervals = gintervals(1), iterator = "dense_track"
)

misha documentation built on Sept. 14, 2023, 5:08 p.m.