Returns the result of track expressions evaluation for each of the iterator intervals.
gextract(
...,
intervals = NULL,
colnames = NULL,
iterator = NULL,
band = NULL,
file = NULL,
intervals.set.out = NULL
)track expression
genomic scope for which the function is applied
sets the columns names in the returned value. If 'NULL' names are set to track expression.
track expression iterator. If 'NULL' iterator is determined implicitly based on track expressions.
track expression band. If 'NULL' no band is used.
file name where the function result is optionally outputted in tab-delimited format
intervals set name where the function result is optionally outputted
If 'file' and 'intervals.set.out' are 'NULL' a set of intervals with an additional column for each of the track expressions and 'columnID' column.
This function returns the result of track expressions evaluation for each of the iterator intervals. The returned value is a set of intervals with an additional column for each of the track expressions. This value can be used as an input for any other function that accepts intervals. If the intervals inside 'intervals' argument overlap gextract returns the overlapped coordinate more than once.
The order inside the result might not be the same as the order of intervals. An additional column 'intervalID' is added to the return value. Use this column to refer to the index of the original interval from the supplied 'intervals'.
If 'file' parameter is not 'NULL' the result is outputted to a tab-delimited text file (without 'intervalID' column) rather than returned to the user. This can be especially useful when the result is too big to fit into the physical memory. The resulted file can be used as an input for 'gtrack.import' or 'gtrack.array.import' functions.
If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Similarly to 'file' parameter 'intervals.set.out' can be useful to overcome the limits of the physical memory.
'colnames' parameter controls the names of the columns that contain the evaluated expressions. By default the column names match the track expressions.
# \dontshow{
options(gmax.processes = 2)
# }
gdb.init_examples()
## get values of 'dense_track' for [0, 500), chrom 1
gextract("dense_track", gintervals(1, 0, 500))
#> chrom start end dense_track intervalID
#> 1 chr1 0 50 0.1777778 1
#> 2 chr1 50 100 0.1600000 1
#> 3 chr1 100 150 0.1800000 1
#> 4 chr1 150 200 0.1600000 1
#> 5 chr1 200 250 0.1600000 1
#> 6 chr1 250 300 0.2000000 1
#> 7 chr1 300 350 0.1600000 1
#> 8 chr1 350 400 0.1600000 1
#> 9 chr1 400 450 0.1600000 1
#> 10 chr1 450 500 0.0600000 1
## get values of 'rects_track' (a 2D track) for a 2D interval
gextract(
"rects_track",
gintervals.2d("chr1", 0, 4000, "chr2", 2000, 5000)
)
#> NULL
## get values of two track expressions 'dense_track' and
## 'array_track * 2' running over '100' iterator
gextract("dense_track", "array_track * 2", gintervals(1, 0, 500),
iterator = 100, colnames = c("expr1", "expr2")
)
#> chrom start end expr1 expr2 intervalID
#> 1 chr1 0 100 0.1688889 8.0000 1
#> 2 chr1 100 200 0.1700000 212.3333 1
#> 3 chr1 200 300 0.1800000 407.2000 1
#> 4 chr1 300 400 0.1600000 NaN 1
#> 5 chr1 400 500 0.1100000 NaN 1