globalSeq.R
In globalSeq: Global Test for Counts

## ----eval=FALSE---------------------------------------------------------------
#  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)