gvtrack.array.slice: Defines rules for a single value calculation of a virtual...

In misha: Toolkit for Analysis of Genomic Data

Defines rules for a single value calculation of a virtual 'Array' track

Description

Defines how a single value within an interval is achieved for a virtual track based on 'Array' track.

Usage

gvtrack.array.slice(vtrack = NULL, slice = NULL, func = "avg", params = NULL)

Arguments

vtrack	virtual track name
slice	a vector of column names or column indices or 'NULL'
func, params	see below

Details

A track (regular or virtual) used in a track expression is expected to return one value for each track interval. 'Array' tracks store multiple values per interval (one for each 'column') and hence if used in a track expression one must define the way of how a single value should be deduced from several ones.

By default if an 'Array' track is used in a track expressions, its interval value would be the average of all column values that are not NaN. 'gvtrack.array.slice' allows to select specific columns and to specify the function applied to their values.

'slice' parameter allows to choose the columns. Columns can be indicated by their names or their indices. If 'slice' is 'NULL' the non-NaN values of all track columns are used.

'func' parameter determines the function applied to the columns' values. Use the following table for a reference of all valid functions and parameters combinations:

func = "avg", params = NULL
Average of columns' values.

func = "max", params = NULL
Maximum of columns' values.

func = "min", params = NULL
Minimum of columns' values.

func = "stdev", params = NULL
Unbiased standard deviation of columns' values.

func = "sum", params = NULL
Sum of columns' values.

func = "quantile", params = [Percentile in the range of [0, 1]]
Quantile of columns' values.

Value

None.

See Also

gvtrack.create, gtrack.array.get_colnames, gtrack.array.extract

Examples

gdb.init_examples()
gvtrack.create("vtrack1", "array_track")
gvtrack.array.slice("vtrack1", c("col2", "col4"), "max")
gextract("vtrack1", gintervals(1, 0, 1000))

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