Evaluates track expression and translates the values into bin indices that are used in turn to retrieve and return values from a lookup table.
glookup(
lookup_table = NULL,
...,
intervals = NULL,
include.lowest = FALSE,
force.binning = TRUE,
iterator = NULL,
band = NULL,
intervals.set.out = NULL
)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
genomic scope for which the function is applied
if 'TRUE', the lowest value of the range determined by breaks is included
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.
track expression iterator. If 'NULL' iterator is determined implicitly based on track expressions.
track expression band. If 'NULL' no band is used.
intervals set name where the function result is optionally outputted
If 'intervals.set.out' is 'NULL' a set of intervals with additional 'value' and 'columnID' columns.
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.
# \dontshow{
options(gmax.processes = 2)
# }
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))
#> chrom start end value intervalID
#> 1 chr1 0 50 4 1
#> 2 chr1 50 100 3 1
#> 3 chr1 100 150 5 1
#> 4 chr1 150 200 3 1
## 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)
)
#> chrom start end value intervalID
#> 1 chr1 0 50 14 1
#> 2 chr1 50 100 3 1
#> 3 chr1 100 150 15 1
#> 4 chr1 150 200 3 1