detail.stats-methods | R Documentation |
This generic function calculates some mixed statistics.
## S4 method for signature 'GENOME' detail.stats( object, new.populations=FALSE, new.outgroup=FALSE, subsites=FALSE, biallelic.structure=FALSE, mismatch.distribution=FALSE, site.spectrum=TRUE, site.FST=FALSE ) ## S4 method for signature 'GENOME' get.detail(object, biallelic.structure=FALSE)
object |
an object of class |
new.populations |
list of populations. |
new.outgroup |
outgroup sequences. |
subsites |
|
biallelic.structure |
fixed and shared polymorphisms (stored in |
mismatch.distribution |
statistics based on mismatch distribution |
site.spectrum |
minor allele frequency of each SNP |
site.FST |
computes FST for each SNP |
The return value is a modified object of class "GENOME"
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The following Slots will be modified in the "GENOME"
object
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MDSD |
... |
MDG1 |
... |
MDG2 |
... |
region.stats |
the slot |
The function get.detail(GENOME.class, biallelic.structure=TRUE)
returns a matrix for each region, where
0 |
population is polymorphic, the remaining individuals are polymorphic |
1 |
population is polymorphic, the remaining individuals are monomorphic |
2 |
population is monomorphic, the remaining individuals are polymorphic |
3 |
population is monomorphic, the remaining individuals are monomorphic with the same value |
4 |
population is monomorphic, the remaining individuals are monomorphic with different values |
# GENOME.class <- readData("\home\Alignments") # GENOME.class # GENOME.class <- set.populations(GENOME.class,list(1:10)) # GENOME.class <- detail.stats(GENOME.class) # show the result: # mismatch.values <- get.detail(GENOME.class) # bial.struc.values <- get.detail(GENOME.class, biallelic.structure=TRUE) # GENOME.class@region.stats@biallelic.structure # GENOME.class@region.stats@biallelic.structure[[1]]
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