plotDeletion() error

[thedam]

Hi,
I think you have something wrong in plotDeletion function.
when I run:

lapply(1:nrow(results$filteredCalls),function(i){
  plotDeletion(results$filteredCalls, i, results$bedOrdered, results$rpkmDtOrdered,  lowRPKMthreshold, plotsDir, mainText=""  )})

I get error:

Error in !calls$inAOH_1000[other_idx] : invalid argument type

I discovered that when I'm setting:
minAOHsize <- 500
the hardcoded variable calls$inAOH_1000 becomes calls$inAOH_500. After changing it manually in the code, everything works.
so when I'm using: minAOHsize <- 500
I have to manually change it:

	if (length(other_idx)>0){
		noAOH <- calls$FID[other_idx][which(!calls$inAOH_1000[other_idx])]
	}

on this:

	if (length(other_idx)>0){
		noAOH <- calls$FID[other_idx][which(!calls$inAOH_500[other_idx])]
	}

(however at the end there are printed such info:

[[121]]
null device
1

[[122]]
null device
1

[[123]]
null device
1

but at least I obtain all 123 plots).

Thanks
Damian Loska