RandomPlacement: Difference between revisions
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(to be done: add image to demonstrate) | (to be done: add image to demonstrate) | ||
*You have a set of non-overlapping items of varying length that are | |||
currently sitting on the genome in their initial locations. These are | currently sitting on the genome in their initial locations. These are | ||
defined with a bed file. | defined with a bed file. | ||
*There is a set of "bounding regions" that define where these items are not | |||
allowed to be. The items are allowed to exist anywhere in the gaps between | allowed to be. The items are allowed to exist anywhere in the gaps between | ||
these bounding regions. When the randomization simulation is done, these | these bounding regions. When the randomization simulation is done, these | ||
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placed. They always remain non-overlapping as they are randomly placed. | placed. They always remain non-overlapping as they are randomly placed. | ||
These bounding regions are defined with a bed file. | These bounding regions are defined with a bed file. | ||
*The distance measurement is done between all the placed items and their | |||
nearest neighbor bounding region. They are measured as they initially sit, | nearest neighbor bounding region. They are measured as they initially sit, | ||
and after randomized placement to determine if they have a different | and after randomized placement to determine if they have a different | ||
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of the placed item, whichever is closer to one of the bounding region | of the placed item, whichever is closer to one of the bounding region | ||
elements. | elements. | ||
*As an alternative for distance measurement instead of to the bounding | |||
regions, a third bed file can be given that is used as items to measure | regions, a third bed file can be given that is used as items to measure | ||
distance to while still within the limitation of being placed inside the | distance to while still within the limitation of being placed inside the | ||
bounding regions. | bounding regions. | ||
Revision as of 22:36, 7 April 2006
randomPlacement description
source tree location: src/hg/randomPlacement/
It helps to draw a picture as you read this to see how it works. (to be done: add image to demonstrate)
- You have a set of non-overlapping items of varying length that are
currently sitting on the genome in their initial locations. These are defined with a bed file.
- There is a set of "bounding regions" that define where these items are not
allowed to be. The items are allowed to exist anywhere in the gaps between these bounding regions. When the randomization simulation is done, these gaps between the bounding regions are where they are allowed to be randomly placed. They always remain non-overlapping as they are randomly placed. These bounding regions are defined with a bed file.
- The distance measurement is done between all the placed items and their
nearest neighbor bounding region. They are measured as they initially sit, and after randomized placement to determine if they have a different measurement after randomization. The distance measured is from either end of the placed item, whichever is closer to one of the bounding region elements.
- As an alternative for distance measurement instead of to the bounding
regions, a third bed file can be given that is used as items to measure distance to while still within the limitation of being placed inside the bounding regions.
