gextract: Returns evaluated track expression

In misha: Toolkit for Analysis of Genomic Data

Returns evaluated track expression

Description

Returns the result of track expressions evaluation for each of the iterator intervals.

Usage

gextract(
  ...,
  intervals = NULL,
  colnames = NULL,
  iterator = NULL,
  band = NULL,
  file = NULL,
  intervals.set.out = NULL
)

Arguments

...	track expression
intervals	genomic scope for which the function is applied
colnames	sets the columns names in the returned value. If 'NULL' names are set to track expression.
iterator	track expression iterator. If 'NULL' iterator is determined implicitly based on track expressions.
band	track expression band. If 'NULL' no band is used.
file	file name where the function result is optionally outputted in tab-delimited format
intervals.set.out	intervals set name where the function result is optionally outputted

Details

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.

Value

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.

See Also

gtrack.array.extract, gsample, gtrack.import, gtrack.array.import, glookup, gpartition, gdist

Examples

gdb.init_examples()

## get values of 'dense_track' for [0, 500), chrom 1
gextract("dense_track", gintervals(1, 0, 500))

## get values of 'rects_track' (a 2D track) for a 2D interval
gextract(
    "rects_track",
    gintervals.2d("chr1", 0, 4000, "chr2", 2000, 5000)
)

## 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")
)

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