summaryLDna: Summerises LD clusters

In petrikemppainen/LDna: Linkage disequilibrum network analysis (LDna)

Summerises LD clusters

Description

Creates a data frame with summary information of LD clusters extracted by function extractBranches

Usage

summaryLDna(ldna, clusters, LDmat)

Arguments

ldna	Output from LDnaRaw
clusters	Output from extractBranches
LDmat	a matrix of pairwise LD values used for LDnaRaw

Value

Returns a data frame with each row corresponding to a cluster, in decreasing order with respect to highest LD threshold value at which they are present. Column "Merge.at" specfies the LD threshold for cluster merger. "Median.LD" gives the median LD of all pairwise values between loci in a cluster, and "MAD.LD" gives their unscaled median absolute deviation.

Author(s)

Petri Kemppainen [e-mail]

See Also

extractBranches, LDnaRaw and plotLDnetwork

Examples

# Simple upper diagonal LD matrix
LDmat <- structure(c(NA, 0.84, 0.64, 0.24, 0.2, 0.16, 0.44, 0.44, NA, NA, 0.8, 0.28, 0.4, 0.36, 0.36, 0.24, NA, NA, NA, 0.48, 0.32, 0.2, 0.36, 0.2, NA, NA, NA, NA, 0.76, 0.56, 0.6, 0.2, NA, NA, NA, NA, NA, 0.72, 0.68, 0.24, NA, NA, NA, NA, NA, NA, 0.44, 0.24, NA, NA, NA, NA, NA, NA, NA, 0.2, NA, NA, NA, NA, NA, NA, NA, NA), .Dim = c(8L, 8L), .Dimnames = list(c("L1", "L2", "L3", "L4", "L5", "L6", "L7", "L8"), c("L1", "L2", "L3", "L4", "L5", "L6", "L7", "L8")))
# Produce neccesary data for LDna
ldna <- LDnaRaw(LDmat)
# Extract clusters and plot graphs, for this small example min.edges is set to zero such that each tip clade corresponds to an individual locus
clusters <- extractBranches(ldna, min.edges=0,merge.min = 0.6)
summary <- summaryLDna(ldna, clusters, LDmat)
summary
## example with baimaii data set
data(LDna)
ldna <- LDnaRaw(r2.baimaii_subs)
clusters <- extractBranches(ldna, min.edges=20,merge.min = 0.6)
summary <- summaryLDna(ldna, clusters, r2.baimaii_subs)
summary

petrikemppainen/LDna documentation built on April 14, 2024, 6:37 p.m.