Description Usage Arguments Value Author(s)
function of searching for the next grouping given deleted SNPs
1 |
lib |
the alleles library contains allele sequences for those only appear in the case and control samples |
lib.names |
the corresponding names of the alleles |
case.sub |
case subjects, two columns for two haplotypes |
ctl.sub |
control subjects, two columns for two haplotypes |
aic.now |
aic for the current model |
dev.now |
deviance for the current model |
df.now |
degree of freedom for the current model |
rank |
numbers of pairs with top similarity scores to be investigate if FALSE, then deviance is calculated for the step-wise merger, then option "alpha" and "step" is used |
cut |
cutoff for similarity score to be consider, default is -1, means all scores above 0 |
delete.snp |
a vector of position of deleted SNPs |
ref |
allele names for the reference level, the default reference level (ref="NA") is the most common allelels |
alpha |
family-wise error, used for deviance only |
step |
index for how many deletions have been carried so far |
del |
position of deleted SNPs |
aic |
AIC |
df |
degree of freedom |
dev |
deviance |
stop |
1: no merge found |
record |
the record of the searching path |
Xin Huang
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