HAP.ror: ROR
In HAP.ROR: Recursive Organizer (ROR)

Description Usage Arguments Details Value Author(s) References Examples

perform ROR for sequence-based association analysis

1	HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha = 0.01, ref.level = NA, display.proc = TRUE)

`case.sub`	case subjects, two columns for two haplotypes
`ctl.sub`	control subjects, two columns for two haplotypes
`lib.sub`	the alleles library contains allele sequences for those only appear in the case and control samples
`lib.sub.names`	the corresponding names of the alleles (mapping of full name in the library and short name in samples)
`alpha`	significance level
`ref.level`	name of the reference allele, "NA" use the most common allele as reference, can also specify allele name, for DRB1, it is "101"
`display.proc`	display the grouping process or not? default is TRUE

This function performs ROR for sequence-based association analysis

`dev.list`	deviances for all steps of ROR
`AIC.list`	AICs for all steps of ROR
`df.list`	degree of freedom for all steps of ROR
`records`	the record of the whole ROR process
`deleted.snps.ls`	the history of SNP deletions for all steps of ROR
`deleted.snps`	the final vector of deleted SNPs
`grp.result`	the final grouping result
`model.summary`	the GLM model summary for the final grouping

Lue Ping Zhao and Xin Huang
Maintainer: Xin Huang <xhuang.fhcrc@gmail.com>

Zhao, L.P. and Huang, X. Recursive organizer (ROR): an analytic framework for sequence-based association analysis. Human Genetics, 2013

library("HAP.ROR")
data(case.sub)
data(ctl.sub)
data(lib.sub)
data(lib.sub.names)
ror.res <- HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha=0.01, ref.level="101");

# grouping result:
round(ror.res$dev.list, 2);
round(ror.res$AIC.list, 2);
ror.res$df.list;
ror.res$deleted.snps;
ror.res$grp.result;
ror.res$significant;
# model summary:
ror.res$model.summary;