data/README.md

In its-likeli-jeff/LLCT: Longitudinal Linear Combination Test for Gene set Analysis

After loadind data_LLCT.rda:

LLCT for unrelated subjects with two time variables (time and time2) defining phenotypic temppral patterns

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time","time2"), covariate=NULL,phenotype="phenotype",familybased=FALSE,pedigree=NULL,FIX.formula="phenotype~time+time2", RANDOM.formula=NULL,nbPermutations=1000)

LLCT for unrelated subjects with a linear time trend

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time"), covariate=NULL,phenotype="phenotype",familybased=FALSE,pedigree=NULL,FIX.formula="phenotype~time", RANDOM.formula=NULL,nbPermutations=1000)

LLCT for unrelated subjects with binary phenotype

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time"), covariate=NULL,phenotype="binary.phenotype",familybased=FALSE,pedigree=NULL,FIX.formula="binary.phenotype~time", RANDOM.formula=NULL,nbPermutations=1000,family="binomial(link=logit)")

LLCT for unrelated subjects with adjustment for time dependent covariate

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time"), covariate="covariate",phenotype="phenotype",familybased=TRUE,pedigree="pedigree",FIX.formula="phenotype~time+covariate", RANDOM.formula="~1|ID",nbPermutations=1000)

LLCT for related subjects with adjustment for time dependent covariate

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time"), covariate="covariate",phenotype="phenotype",familybased=TRUE,pedigree="pedigree",FIX.formula="phenotype~time+covariate", RANDOM.formula="~1|ID",nbPermutations=1000)

LLCT for related subjects with adjustment for more complex time trend

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time","time2"), covariate="covariate",phenotype="phenotype",familybased=TRUE,pedigree="pedigree",FIX.formula="phenotype~time+time2", RANDOM.formula="~1|ID",nbPermutations=1000)

LLCT for related subjects with binary phenotype

LLCT(EXPR=EXPR, GS=GS, LongData=LongData, ID="ID",time=c("time"), covariate="covariate",phenotype="binary.phenotype",familybased=TRUE,pedigree="pedigree",FIX.formula="binary.phenotype~time", RANDOM.formula="~1|ID",nbPermutations=1000,family="binomial(link=logit)")

its-likeli-jeff/LLCT documentation built on Nov. 4, 2019, 2:13 p.m.