misha-package: Toolkit for analysis of genomic data
In misha: Toolkit for Analysis of Genomic Data

misha-package

R Documentation

Toolkit for analysis of genomic data

'misha' package is intended to help users to efficiently analyze genomic data achieved from various experiments.

For a complete list of help resources, use library(help = "misha").

The following options are available for the package. Use 'options' function to alter the value of the options.

NAME	DEFAULT	DESCRIPTION
gmax.data.size	AUTO	Auto-configured based on system RAM and processes.
		Formula: min((RAM * 0.7) / gmax.processes, 10GB).
		Prevents excessive memory usage by 'gextract', 'gscreen', etc.
gbig.intervals.size	1000000	Minimal number of intervals in a big intervals set format
gmax.mem.usage	10000000	Maximal memory consumption of all child processes in KB before
		the limiting algorithm is invoked.
gmax.processes	AUTO	Auto-configured to 70% of CPU cores.
		Maximal number of processes for multitasking.
gmax.processes2core	2	Maximal number of processes per CPU core for multitasking
gmin.scope4process	10000	Minimal scope range (for 2D: surface) assigned to a process
		in multitasking mode.
gbuf.size	1000	Size of track expression values buffer.
gtrack.chunk.size	100000	Chunk size in bytes of a 2D track. If '0' chunk size
		is unlimited.
gtrack.num.chunks	0	Maximal number of 2D track chunks simultaneously stored
		in memory.
gmultitasking	TRUE	Enable/disable automatic parallelization. Small datasets
		(< gmax.processes * 1000 records) use single-threaded mode.

More information about the options can be found in 'User manual' of the package.

Maintainer: Aviezer Lifshitz aviezer.lifshitz@weizmann.ac.il

Authors:

Other contributors: