epsout.ld.snp
(Package: chopsticks) :
Function to write an eps file directly to visualize LD
epsout.ld.snp takes an object of snp.matrix class and a given snp range and depth, draw a eps file to visualize the LD in the same color scheme as haploview's default view. It was the first prototype of this bunch of software. Also, it does not keep any pair-wise data in memory at all, and maybe more suitable where the actual pair-wise LD data is not needed.
To carry out a score test for a GLM, we first fit a "base" model using the standard iteratively reweighted least squares (IRLS) algorithm and then carry out a score test for addition of further terms. This function sets various control parameters for this.
ibs.stats
(Package: chopsticks) :
function to calculate the identity-by-state stats of a group
Given a snp.matrix-class or a X.snp.matrix-class object with $N$ samples, calculates some statistics about the relatedness of every pair of samples within.
ibsDist
(Package: chopsticks) :
Distance matrix based on identity by state (IBS)
Expresses a matrix of IBS counts (see ibsCount) as a distance matrix. The distance between two samples is returned as the proportion of allele comparisons which are not IBS.
ld.snp
(Package: chopsticks) :
Function to calculate pairwise D', $r^2$
ld.snp takes an object of snp.matrix class and suitable range and depth and calculation the pairwise D', $r^2$, LOD and return the result as a snp.dprime object.
providing 
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