ROR

Description

perform ROR for sequence-based association analysis

Usage

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

Arguments

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

Details

This function performs ROR for sequence-based association analysis

Value

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

Author(s)

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

References

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

Examples

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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;