## ------------------------------------------------------------------------
library(DEGreport)
data(humanSexDEedgeR)
library(edgeR)


## ------------------------------------------------------------------------
des<-humanSexDEedgeR$design
fit <- glmFit(humanSexDEedgeR,des)
lrt <- glmLRT(fit)
tab<-cbind(lrt$table,p.adjust(lrt$table$PValue,method="BH"))
detags <- rownames(tab[tab[,5]<=0.1,])
plotSmear(humanSexDEedgeR, de.tags=detags)


## ------------------------------------------------------------------------
counts<-cpm(humanSexDEedgeR,log=FALSE)
g1<-colnames(counts)[1:41]
g2<-colnames(counts)[42:85]
design<-data.frame(condition=sub("1","Male",sub("0","Female",des[,2])))



## ------------------------------------------------------------------------
library(biomaRt)
mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
g = getGene( id = detags, type = "ensembl_gene_id", mart = mart)
colors=data.frame(genes=g$ensembl_gene_id,colors=sub("[1-9]{1,2}","Autosomic",g$chromosome_name))


## ------------------------------------------------------------------------
#un comment the las code to create the html
detag10<-detags[1:10]
pval<-tab[,4]
fc<-tab[detag10,1]


## ----eval=FALSE----------------------------------------------------------
## 
## pathreport<-"~/report"
## createReport(g1,g2,counts,detag10,pval,fc,pathreport,colors,pop=400)


## ----eval=FALSE----------------------------------------------------------
## degObj(counts,design,"/tmp/degObj.rda")
## library(shiny)
## runGist(9930881)
## 


## ----dev='jpeg'----------------------------------------------------------
degMean(pval,counts)
degVar(pval,counts)
degMV(g1,g2,pval,counts)
degMB(detags,g1,g2,counts)
degVB(detags,g1,g2,counts)
rank<-degRank(g1,g2,counts[detag10,],fc,400,500)
degPR(rank)