Documentation for Chromosome class from SLiM
This class represents the layout and properties of the chromosome being simulated. The chromosome currently being simulated is available through the sim.chromosome global. Section 1.5.4 presents an overview of the conceptual role of this class. This class has the following methods (functions):
This class has the following properties:
A property of type string. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: The color used to display substitutions in SLiMgui when both mutations and substitutions are being displayed in the chromosome view. Outside of SLiMgui, this property still exists, but is not used by SLiM. Colors may be specified by name, or with hexadecimal RGB values of the form "#RRGGBB" (see the Eidos manual). If colorSubstitution is the empty string, "", SLiMgui will defer to the color scheme of each MutationType, just as it does when only substitutions are being displayed. The default, "3333FF", causes all substitutions to be shown as dark blue when displayed in conjunction with mutations, to prevent the view from becoming too noisy. Note that when substitutions are displayed without mutations also being displayed, this value is ignored by SLiMgui and the substitutions use the color scheme of each MutationType.
A property of type logical. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: When gene conversion has been enabled by calling initializeGeneConversion(), switching to the DSB recombination model, this property is T; otherwise, when using the crossover breakpoints model, it is F.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The gene conversion bias coefficient, which expresses a bias in the resolution of heteroduplex mismatches in complex gene conversion tracts. When gene conversion has not been enabled by calling initializeGeneConversion(), this property will be unavailable.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The fraction of double-stranded breaks that result in non-crossover events. When gene conversion has not been enabled by calling initializeGeneConversion(), this property will be unavailable.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The mean length of a gene conversion tract (in base positions). When gene conversion has not been enabled by calling initializeGeneConversion(), this property will be unavailable.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The fraction of gene conversion tracts that are "simple" (i.e., not involving resolution of heteroduplex mismatches); the remainder will be "complex". When gene conversion has not been enabled by calling initializeGeneConversion(), this property will be unavailable.
A property of type GenomicElement object. This property is a constant, so it is not modifiable. Property Description: All of the GenomicElement objects that comprise the chromosome.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for hotspot map regions along the chromosome. Each hotspot map region is assumed to start at the position following the end of the previous hotspot map region; in other words, the regions are assumed to be contiguous. When using sex-specific hotspot maps, this property will unavailable; see hotspotEndPositionsF and hotspotEndPositionsM.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for hotspot map regions for females, when using sex-specific hotspot maps; unavailable otherwise. See hotspotEndPositions for further explanation.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for hotspot map regions for males, when using sex-specific hotspot maps; unavailable otherwise. See hotspotEndPositions for further explanation.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The hotspot multiplier for each of the hotspot map regions specified by hotspotEndPositions. When using sex-specific hotspot maps, this property will be unavailable; see hotspotMultipliersF and hotspotMultipliersM.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The hotspot multiplier for each of the hotspot map regions specified by hotspotEndPositionsF, when using sex-specific hotspot maps; unavailable otherwise.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The hotspot multiplier for each of the hotspot map regions specified by hotspotEndPositionsM, when using sex-specific hotspot maps; unavailable otherwise.
A property of type integer. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The last valid position in the chromosome; its length, essentially. Note that the chromosome length is determined by the maximum of the end of the last genomic element, the end of the last recombination region, and the end of the last mutation map region (or hotspot map region).
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for mutation rate regions along the chromosome. Each mutation rate region is assumed to start at the position following the end of the previous mutation rate region; in other words, the regions are assumed to be contiguous. When using sex-specific mutation rate maps, this property will unavailable; see mutationEndPositionsF and mutationEndPositionsM. This property is unavailable in nucleotide-based models.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for mutation rate regions for females, when using sex-specific mutation rate maps; unavailable otherwise. See mutationEndPositions for further explanation. This property is unavailable in nucleotide-based models.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for mutation rate regions for males, when using sex-specific mutation rate maps; unavailable otherwise. See mutationEndPositions for further explanation. This property is unavailable in nucleotide-based models.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The mutation rate for each of the mutation rate regions specified by mutationEndPositions. When using sex-specific mutation rate maps, this property will be unavailable; see mutationRatesF and mutationRatesM. This property is unavailable in nucleotide-based models.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The mutation rate for each of the mutation rate regions specified by mutationEndPositionsF, when using sex-specific mutation rate maps; unavailable otherwise. This property is unavailable in nucleotide-based models.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The mutation rate for each of the mutation rate regions specified by mutationEndPositionsM, when using sex-specific mutation rate maps; unavailable otherwise. This property is unavailable in nucleotide-based models.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The overall mutation rate across the whole chromosome determining the overall number of mutation ranges and rates as well as the coverage of the chromosome by genomic elements (since mutations are only generated within genomic elements, regardless of the mutation rate map). When using sexspecific mutation rate maps, this property will unavailable; see overallMutationRateF and overallMutationRateM. This property is unavailable in nucleotide-based models.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The overall mutation rate for females, when using sex-specific mutation rate maps; unavailable otherwise. See overallMutationRate for further explanation. This property is unavailable in nucleotide-based models.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The overall mutation rate for males, when using sex-specific mutation rate maps; unavailable otherwise. See overallMutationRate for further explanation. This property is unavailable in nucleotide-based models.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The overall recombination rate across the whole chromosome determining the overall number of recombination events that will occur anywhere in the chromosome, as calculated from the individual recombination ranges and rates. When using sex-specific recombination maps, this property will unavailable; see overallRecombinationRateF and overallRecombinationRateM.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The overall recombination rate for females, when using sex-specific recombination maps; unavailable otherwise. See overallRecombinationRate for further explanation.
A property of type float. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The overall recombination rate for males, when using sex-specific recombination maps; unavailable otherwise. See overallRecombinationRate for further explanation.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for recombination regions along the chromosome. Each recombination region is assumed to start at the position following the end of the previous recombination region; in other words, the regions are assumed to be contiguous. When using sex-specific recombination maps, this property will unavailable; see recombinationEndPositionsF and recombinationEndPositionsM.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for recombination regions for females, when using sex-specific recombination maps; unavailable otherwise. See recombinationEndPositions for further explanation.
A property of type integer. This property is a constant, so it is not modifiable. Property Description: The end positions for recombination regions for males, when using sex-specific recombination maps; unavailable otherwise. See recombinationEndPositions for further explanation.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The recombination rate for each of the recombination regions specified by recombinationEndPositions. When using sex-specific recombination maps, this property will unavailable; see recombinationRatesF and recombinationRatesM.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The recombination rate for each of the recombination regions specified by recombinationEndPositionsF, when using sex-specific recombination maps; unavailable otherwise.
A property of type float. This property is a constant, so it is not modifiable. Property Description: The recombination rate for each of the recombination regions specified by recombinationEndPositionsM, when using sex-specific recombination maps; unavailable otherwise.
A property of type Species object. It is of length one (a singleton). This property is a constant, so it is not modifiable. Property Description: The species to which the target object belongs.
A property of type integer. It is of length one (a singleton). This property is a variable, so it is modifiable. Property Description: A user-defined integer value. The value of tag is initially undefined, and it is an error to try to read it; if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code. The value of tag is not used by SLiM; it is free for you to use.
Other Chromosome:
ancestralNucleotides(),
drawBreakpoints(),
setAncestralNucleotides(),
setGeneConversion(),
setHotspotMap(),
setMutationRate(),
setRecombinationRate()