gtrack.create_pwm_energy: Creates a new track from PSSM energy function

In misha: Toolkit for Analysis of Genomic Data

Creates a new track from PSSM energy function

Description

Creates a new track from PSSM energy function.

Usage

gtrack.create_pwm_energy(
  track = NULL,
  description = NULL,
  pssmset = NULL,
  pssmid = NULL,
  prior = NULL,
  iterator = NULL
)

Arguments

track	track name
description	a character string description
pssmset	name of PSSM set: 'pssmset.key' and 'pssmset.data' must be presented in 'GROOT/pssms' directory
pssmid	PSSM id
prior	prior
iterator	track expression iterator for the newly created track

Details

This function creates a new track with values of a PSSM energy function. PSSM parameters (nucleotide probability per position and pluralization) are determined by 'pssmset' key and data files ('pssmset.key' and 'pssmset.data'). These two files must be located in 'GROOT/pssms' directory. The type of the created track is determined by the type of the iterator. 'description' is added as a track attribute.

Value

None.

See Also

gtrack.create, gtrack.2d.create, gtrack.create_sparse, gtrack.smooth, gtrack.modify, gtrack.rm, gtrack.info, gdir.create

Examples

gdb.init_examples()
gtrack.create_pwm_energy("pwm_energy_track", "Test track", "pssm",
    3, 0.01,
    iterator = 100
)
gextract("pwm_energy_track", gintervals(1, 0, 1000))

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