RandomPlacement: Difference between revisions

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(to be done: add image to demonstrate)
(to be done: add image to demonstrate)


<ol>
*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.
<li>You have a set of non-overlapping items of varying length that are
*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.
currently sitting on the genome in their initial locations.  These are
*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.
defined with a bed file.
*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.
<li>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
[[Category:Technical FAQ]]
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.
<li>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.
<li>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.
</ol>

Latest revision as of 18:37, 8 May 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.