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).
		Controls max in-memory result buffer size for streaming/sampling.
		Operations like gextract, gscreen use this as upper bound.
gbig.intervals.size	1000000	Threshold for converting interval sets to disk-based
		"big" format. When interval count exceeds this, intervals
		are stored per-chromosome instead of all in memory.
		Note: Independent of gmax.data.size (different purposes).
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.
gmultitask.max.records.factor	64	Multiplier to inflate multitask
		max_records estimates to avoid under-allocation.
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. Some functions
		may choose single-threaded mode for very small workloads.

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

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

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