gintervals.summary: Calculates summary statistics of track expression for...

In misha: Toolkit for Analysis of Genomic Data

Calculates summary statistics of track expression for intervals

Description

Calculates summary statistics of track expression for intervals.

Usage

gintervals.summary(
  expr = NULL,
  intervals = NULL,
  iterator = NULL,
  band = NULL,
  intervals.set.out = NULL
)

Arguments

expr	track expression
intervals	set of intervals
iterator	track expression iterator. If 'NULL' iterator is determined implicitly based on track expression.
band	track expression band. If 'NULL' no band is used.
intervals.set.out	intervals set name where the function result is optionally outputted

Details

This function returns summary statistics of a track expression for each interval 'intervals': total number of bins, total number of bins whose value is NaN, min, max, sum, mean and standard deviation of the values.

If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Use this parameter if the result size exceeds the limits of the physical memory.

Value

If 'intervals.set.out' is 'NULL' a set of intervals with additional columns representing summary statistics for each percentile and interval.

See Also

gsummary, gbins.summary

Examples

gdb.init_examples()
intervs <- gintervals(c(1, 2), 0, 5000)
gintervals.summary("dense_track", intervs)

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