## ---------------------------------------------------------------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("globalSeq") ## ------------------------------------------------------------------------ library(globalSeq) ## ----eval=FALSE---------------------------------------------------------- # attach(toydata) ## ----echo=FALSE---------------------------------------------------------- names <- names(toydata) for(i in 1:length(names)){ assign(names[i], toydata[[i]]) } rm(names) ## ----eval=FALSE---------------------------------------------------------- # utils::help(globalSeq) # utils::vignette("globalSeq") ## ------------------------------------------------------------------------ cbind(y,X) ## ------------------------------------------------------------------------ set.seed(1) omnibus(y,X) ## ------------------------------------------------------------------------ rbind(y,offset) ## ------------------------------------------------------------------------ set.seed(1) omnibus(y,X,offset=offset) ## ------------------------------------------------------------------------ rbind(y,group) ## ------------------------------------------------------------------------ set.seed(1) omnibus(y,X,group=group) ## ------------------------------------------------------------------------ set.seed(1) omnibus(y,X,phi=0) ## ------------------------------------------------------------------------ X1 <- X[,c(1:11,15)] X2 <- X[,12:14] ## ------------------------------------------------------------------------ set.seed(1) omnibus(y,list(X1,X2)) ## ----results='hide'------------------------------------------------------ omnibus(y,X,kind=1) # crude permutation test omnibus(y,X,kind=0.05) # interrupting permutation omnibus(y,X,kind=0) # method of control variables ## ----results='hide',fig.width=5,fig.height=2.5,fig.show='hold'----------- proprius(y,X,type="samples") proprius(y,X,type="covariates") ## ----results='hide',fig.width=5,fig.height=3,fig.show='hold'------------- proprius(y,X,type="covariates",alpha=0.05) ## ------------------------------------------------------------------------ cbind(Yloc,Ychr,Y) cbind(Vloc,Vchr,V) cbind(Wloc,Wchr,W) ## ----echo=FALSE---------------------------------------------------------- for(i in 1:length(Yloc)){ cat(paste(names(Yloc[i]),": ",sep="")) cat(names(Vloc)[Yloc[i]-5 < Vloc & Vloc < Yloc[i]+5],"\n") } ## ----results='hide',message=FALSE---------------------------------------- set.seed(1) cursus(Y,Yloc,V,Vloc,window=5) ## ----results='hide',message=FALSE---------------------------------------- set.seed(1) cursus(Y,Yloc,V,Vloc,window=5,Ychr,Vchr) ## ----results='hide',message=FALSE---------------------------------------- offset <- colSums(Y) # library sizes set.seed(1) cursus(Y,Yloc,V,Vloc,window=5,offset=offset) ## ----message=FALSE------------------------------------------------------- set.seed(1) cursus(Y,Yloc,list(V,W),list(Vloc,Wloc),list(5,50)) ## ----eval=FALSE---------------------------------------------------------- # list <- edgeR::DGEList(Y) # list <- edgeR::calcNormFactors(list) # list <- edgeR::estimateDisp(list) # # lib.size <- colSums(Y) # offset <- lib.size/exp(mean(log(lib.size))) # norm.factors <- list$samples$norm.factors # offset <- norm.factors*offset # # phi <- list$tagwise.dispersion # # cursus(Y,Yloc,V,Vloc,window=5,offset=offset,phi=phi)