I have tried to find a beginners guide/tutorial on how to do a paired analysis in Ballgown.
I have several samples pre and post treatment:

ID<- seq(1,170, by=1) 
cond<-rep(c("post","pre"),85) 
pair<- rep(1:85, each = 2) 
design_matrix <- data.frame(id=ID,cond=cond, pair=factor(pair))

For paired analysis, am I right that I run the following? (after creating a ballgown object bg)

pData(bg)=design_matrix
paired<- stattest(bg, feature='transcript', meas='FPKM', covariate='cond', adjustvars='pair')