Question: summarizeOverlap in systemPipeR not working!
0
gravatar for Parham
3.9 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

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!

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Parham1.4k

Problem solved!

ADD REPLYlink written 3.9 years ago by Parham1.4k

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.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Sean Davis25k
1

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

ADD REPLYlink written 3.9 years ago by Parham1.4k
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