output and plot for ROR result

Description

function for output tables and figures related to ROR result

Usage

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ODS.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, records, dev.list, AIC.list, deleted.snps.ls, proteinf, locus = "DRB1*", ref.level = "101")

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)

records

the record of the whole ROR process

dev.list

deviances for all steps of ROR

AIC.list

AICs for all steps of ROR

deleted.snps.ls

the history of SNP deletions for all steps of ROR

proteinf

amino acid matrix for the currsponding alleles

locus

name of locus

ref.level

name of reference allele

Author(s)

Xin Huang

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$model.summary;
# output tables and figures used for ror result
data(proteinf)
ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev.list, AIC.list=ror.res$AIC.list, deleted.snps.ls=ror.res$deleted.snps.ls, proteinf=proteinf, locus="DRB1*", ref.level="101");
cat("ROR result tables/figures are store in folder:", getwd(),"\n")