ODS.ror: output and plot for ROR result

In HAP.ROR: Recursive Organizer (ROR)

Description

function for output tables and figures related to ROR result

Usage

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

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")

HAP.ROR documentation built on May 1, 2019, 10:24 p.m.