summarizeOverlap in systemPipeR not working!

Question

[Parham]

Hi,

I am working with systemPipeR software. In section 5.1 there is a line of code that seems I cannot make it run.

counteByg <- bplapply(bfl, function(x) summarizeOverlaps(eByg, x, mode="Union",
+ ignore.strand=TRUE,
+ inter.feature=FALSE,
+ singleEnd=TRUE))

When I check counteByg for each BAM file it says that it cannot find summarizeOverlaps function

$tag12_PA01BR3.bam
[1] "Error in FUN(...): could not find function \"summarizeOverlaps\"\n"
attr(,"class")

What am I doing wrong?

I have GenomicFeatures and GenomicAlignments loaded definitely!

Thanks in advance!

[Parham]

Problem solved!

[Sean Davis]

Great to hear that your problem is solved. There is no shame in answering your own question, so please take a moment to post your solution so others can benefit.

[Parham]

Yes, I didn't set multicoreParam. I thought the program will continue with defaults but it was not like that.