gtrack.lookup: Creates a new track from a lookup table based on track...

In misha: Toolkit for Analysis of Genomic Data

Creates a new track 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 values from a lookup table and create a track.

Usage

gtrack.lookup(
  track = NULL,
  description = NULL,
  lookup_table = NULL,
  ...,
  include.lowest = FALSE,
  force.binning = TRUE,
  iterator = NULL,
  band = NULL
)

Arguments

track	track name
description	a character string description
lookup_table	a multi-dimensional array containing the values that are returned by the function
...	pairs of track expressions and breaks
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.

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 create with its values a new track. 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' the 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 the value in the track would be 'NaN' too.

'description' is added as a track attribute.

Value

None.

See Also

glookup, gtrack.2d.create, gtrack.create_sparse, gtrack.smooth, gtrack.modify, gtrack.rm, gtrack.info, gdir.create

Examples

gdb.init_examples()

## one-dimensional example
breaks1 <- seq(0.1, 0.2, length.out = 6)
gtrack.lookup(
    "lookup_track", "Test track", 1:5, "dense_track",
    breaks1
)
gtrack.rm("lookup_track", force = TRUE)

## two-dimensional example
t <- array(1:15, dim = c(5, 3))
breaks2 <- seq(0.31, 0.37, length.out = 4)
gtrack.lookup(
    "lookup_track", "Test track", t, "dense_track",
    breaks1, "2 * dense_track", breaks2
)
gtrack.rm("lookup_track", force = TRUE)

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