This generic function calculates the linkage disequilibrium between regions.
# S4 method for GENOME
mult.linkage.stats(object,lower.bound=0,upper.bound=1,pairs=FALSE)an object of class "GENOME"
sites with minor-allele-frequency>=lower.bound are considered
sites with minor-allele-frequency<=upper.bound are considered
permutation matrix of pairwise comparisons
The return value is a modified object of class "GENOME"
--------------------------------------------------------------
The following slots will be modified in the "GENOME" object
--------------------------------------------------------------
Some linkage statistics for each pair of regions (R2, P-value, Distance)
pairs is a matrix. Each column contains the pairwise comparison region IDs.
1 1 2 3
compares region 1 with 2, and region 1 with 3.
# NOT RUN {
# GENOME.class <- readData("...\Alignments")
# GENOME.class
# GENOME.class <- mult.linkage.stats(GENOME.class)
# show the result:
# GENOME.class@mult.Linkage
# }
Run the code above in your browser using DataLab