glookup: Returns values from a lookup table based on track expression

In misha: Toolkit for Analysis of Genomic Data

Returns values from a lookup table based on track expression

Description

Evaluates track expression and translates the values into bin indices that are used in turn to retrieve and return values from a lookup table.

Usage

glookup(
  lookup_table = NULL,
  ...,
  intervals = NULL,
  include.lowest = FALSE,
  force.binning = TRUE,
  iterator = NULL,
  band = NULL,
  intervals.set.out = NULL
)

Arguments

lookup_table	a multi-dimensional array containing the values that are returned by the function
...	pairs of 'expr', 'breaks' where 'expr' is a track expression and the breaks determine the bin
intervals	genomic scope for which the function is applied
include.lowest	if 'TRUE', the lowest value of the range determined by breaks is included
force.binning	if 'TRUE', the values smaller than the minimal break will be translated to index 1, and the values that exceed the maximal break will be translated to index N-1 where N is the number of breaks. If 'FALSE' the out-of-range values will produce NaN values.
iterator	track expression iterator. If 'NULL' iterator is determined implicitly based on track expressions.
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 evaluates the track expression for all iterator intervals and translates this value into an index based on the breaks. This index is then used to address the lookup table and return the according value. More than one 'expr'-'breaks' pair can be used. In that case 'lookup_table' is addressed in a multidimensional manner, i.e. 'lookup_table[i1, i2, ...]'.

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' then the lowest value is included in the first interval, i.e. in [x1, x2].

'force.binning' parameter controls what should be done when the value of 'expr' exceeds the range determined by 'breaks'. If 'force.binning' is 'TRUE' then values smaller than the minimal break will be translated to index 1, and the values exceeding the maximal break will be translated to index 'M-1' where 'M' is the number of breaks. If 'force.binning' is 'FALSE' the out-of-range values will produce 'NaN' values.

Regardless of 'force.binning' value if the value of 'expr' is 'NaN' then result is 'NaN' too.

The order inside the result might not be the same as the order of intervals. Use 'intervalID' column to refer to the index of the original interval from the supplied 'intervals'.

If 'intervals.set.out' is not 'NULL' the result (without 'columnID' column) 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 'value' and 'columnID' columns.

See Also

gtrack.lookup, gextract, gpartition, gdist

Examples

gdb.init_examples()

## one-dimensional lookup table
breaks1 <- seq(0.1, 0.2, length.out = 6)
glookup(1:5, "dense_track", breaks1, gintervals(1, 0, 200))

## two-dimensional lookup table
t <- array(1:15, dim = c(5, 3))
breaks2 <- seq(0.31, 0.37, length.out = 4)
glookup(
    t, "dense_track", breaks1, "2 * dense_track", breaks2,
    gintervals(1, 0, 200)
)

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