Calculates summary statistics of track expression for intervals

Calculates summary statistics of track expression for intervals.

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

Value

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

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.

See also

gsummary, gbins.summary

Examples

# \dontshow{
options(gmax.processes = 2)
# }

gdb.init_examples()
intervs <- gintervals(c(1, 2), 0, 5000)
gintervals.summary("dense_track", intervs)
#>   chrom start  end Total intervals NaN intervals Min  Max      Sum       Mean
#> 1  chr1     0 5000             100             0   0 0.26 5.117778 0.05117778
#> 2  chr2     0 5000             100             0   0 0.34 8.700000 0.08700000
#>      Std dev
#> 1 0.05596612
#> 2 0.07818006