Returns values from 'Array' track

Returns values from 'Array' track.

gtrack.array.extract(
  track = NULL,
  slice = NULL,
  intervals = NULL,
  file = NULL,
  intervals.set.out = NULL
)

Arguments

track

track name

slice

a vector of column names or column indices or 'NULL'

intervals

genomic scope for which the function is applied

file

file name where the function result is to be saved. If 'NULL' result is returned to the user.

intervals.set.out

intervals set name where the function result is optionally outputted

Value

If 'file' and 'intervals.set.out' are 'NULL' a set of intervals with additional columns for 'Array' track column values and 'columnID'.

Details

This function returns the column values of an 'Array' track in the genomic scope specified by 'intervals'. 'slice' parameter determines which columns should appear in the result. The columns can be indicated by their names or their indices. If 'slice' is 'NULL' the values of all track columns are returned.

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 saved 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.array.import' function.

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.

See also

gextract, gtrack.array.get_colnames, gtrack.array.import

Examples

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

gdb.init_examples()
gtrack.array.extract(
    "array_track", c("col3", "col5"),
    gintervals(1, 0, 2000)
)
#>   chrom start  end col3 col5 intervalID
#> 1  chr1     0   50  NaN  NaN          1
#> 2  chr1   100  150  NaN  105          1
#> 3  chr1   250  300  203  NaN          1
#> 4  chr1  1400 1450  303  305          1