Last data update: 2014.03.03
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R: Linkage statistics (R2, P-value, Distance)
calc.R2-methods | R Documentation |
Linkage statistics (R2, P-value, Distance)
Description
This generic function calculates some linkage disequilibrium statistics.
Usage
## S4 method for signature 'GENOME'
calc.R2(object,subsites=FALSE,lower.bound=0,upper.bound=1)
Arguments
object |
an object of class "GENOME"
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subsites |
same as in the other modules
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lower.bound |
sites with minor-allele-frequency>=lower.bound are considered
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upper.bound |
sites with minor-allele-frequency<=upper.bound are considered
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Details
Note, the pairwise comparisons are computed via combn(n.snps,2) .
Value
The slot GENOME.class@region.stats@linkage.disequilibrium will be filled.
(R2,P-value,Distance)
Fisher's Exact Test is used for the P-values.
Examples
# GENOME.class <- readData("...Alignments")
# GENOME.class
# GENOME.class <- calc.R2(GENOME.class)
# show the result:
# GENOME.class@region.stats@linkage.disequilibrium
# [[x]][[y]] x:region, y:population
Results
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