Circ.test: Circ.test
In dieterich-lab/CircTest: Test circRNA dependence on host genes

Description Usage Arguments Examples

Test the independent variation of circRNAs in relevant to their host genes.

1 2	Circ.test(Circ, Linear, CircCoordinates = None, group, alpha = 0.05, plotsig = T, circle_description = c(1:3))

`Circ`	CircRNACount file. A file of circRNA read count table. First three columns are circRNA coordinates, and followed by columns for circRNA read counts, each sample per column.
`Linear`	LinearCount file. A file of circRNA host gene expression count table. Same configuration as CircRNACount file.
`group`	A vector of group indicators.
`alpha`	p value cut off. Defaul 0.05.
`plotsig`	If 'TRUE', significantly host-independently regulated circRNAs will be ploted.
`circle_description`	Column indices which do not carry circle/linear read counts.
`(Optional)`	CircCoordinates BED format circRNA coordinates file.

data(Circ)
data(Linear)
test=Circ.test(Circ=Circ,Linear=Linear,group=c(rep(1,6),rep(2,6),rep(3,6)))
View(test$sig.dat)
# Plot one of them
Circ.ratioplot(Circ,Linear,Coordinates,plotrow=rownames(test$sig.dat)[1],groupindicator1=c(rep('1days',6),rep('4days',6),rep('20days',6)),groupindicator2=rep(c(rep('Female',4),rep('Male',2)),3),lab_legend='Ages', circle_description = c(1:3))