'misha' package is intended to help users to efficiently analyze genomic data achieved from various experiments.
Details
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 min(32, 70% of CPU cores). |
| Maximal number of processes for multitasking. | ||
| gmax.processes2core | 2 | Maximal number of processes per CPU core for multitasking |
| gseq.extract.probe.usec | 100 | gseq.extract times its first reads |
| and distributes across processes when the measured cost per | ||
| interval reaches this many microseconds. 0 always distributes, | ||
| a large value never does. | ||
| 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.
Author
Maintainer: Aviezer Lifshitz aviezer.lifshitz@weizmann.ac.il
Authors:
Aviezer Lifshitz aviezer.lifshitz@weizmann.ac.il
Misha Hoichman misha@hoichman.com
Eitan Yaffe eitan.yaffe@weizmann.ac.il
Amos Tanay amos.tanay@weizmann.ac.il
Other contributors:
Weizmann Institute of Science [copyright holder]