gbins.quantiles: Calculates quantiles of a track expression for bins

In misha: Toolkit for Analysis of Genomic Data

Calculates quantiles of a track expression for bins

Description

Calculates quantiles of a track expression for bins.

Usage

gbins.quantiles(
  ...,
  expr = NULL,
  percentiles = 0.5,
  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 quantiles are calculated
percentiles	an array of percentiles of quantiles in [0, 1] range
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 'gquantiles'. For each iterator interval the value of 'bin_expr' is calculated and assigned to the corresponding bin determined by 'breaks'. The quantiles 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 quantiles for each percentile and bin.

See Also

gquantiles, gintervals.quantiles, gdist

Examples

gdb.init_examples()
gbins.quantiles("dense_track", c(0, 0.2, 0.4, 2), "sparse_track",
    percentiles = c(0.2, 0.5),
    intervals = gintervals(1),
    iterator = "dense_track"
)

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