Hello everyone,

Maybe "I've found an error running summarizeOverlaps()" ...

This is what the example in summarizeOverlaps() does:
-------------------------------------------------------------------------------------------------------------------------
> 
> ## paired-end reads 
> ##
> 
> library("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
> exbygene <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene")
> fl <- system.file("extdata", "untreated3_chr4.bam", 
>     package="pasillaBamSubset") 
> 
> ## Paired-end reads are stored in a GappedAlignmentPairs object
> reads <- readGappedAlignmentPairs(fl)
> 
> res <- summarizeOverlaps(exbygene, reads, "Union")
> stopifnot(length(assays(res)$counts) == length(exbygene))
> 
> -------------------------------------------------------------------------------


I run exactly the same example but with ignore.strand = TRUE. 
Then it gives an error:


> > library("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
> > exbygene <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene")
> > fl <- system.file("extdata", "untreated3_chr4.bam", 
> +     package="pasillaBamSubset") 
> > 
> > ## Paired-end reads are stored in a GappedAlignmentPairs object
> > reads <- readGappedAlignmentPairs(fl)
> 
> >> res <- summarizeOverlaps(exbygene, reads, "Union", ignore.strand = TRUE)
> >Error in .local(x, ..., value) : 
>   replacement 'value' is not an AtomicList with the same elementLengths as 'x'
> >> traceback()
> >7: stop("replacement 'value' is not an AtomicList with the same ", 
>        "elementLengths as 'x'")
> >6: .local(x, ..., value)
> >5: `strand<-`(`*tmp*`, value = "*")
> >4: `strand<-`(`*tmp*`, value = "*")
> >3: .dispatchOverlaps(grglist(reads), features, mode, ignore.strand)
> >2: summarizeOverlaps(exbygene, reads, "Union", ignore.strand = TRUE)
> >1: summarizeOverlaps(exbygene, reads, "Union", ignore.strand = TRUE)
> 
> 
> >>  sessionInfo()
> >R version 2.15.1 (2012-06-22)
> >Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> >locale:
> > [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C              
> > [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
> > [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8   
> > [7] LC_PAPER=C                 LC_NAME=C                 
> > [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       
> 
> >attached base packages:
> >[1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> >other attached packages:
> >[1] Rsamtools_1.9.25                         
> > [2] Biostrings_2.25.8                        
> > [3] rtracklayer_1.17.15                      
> > [4] TxDb.Dmelanogaster.UCSC.dm3.ensGene_2.7.1
> > [5] GenomicFeatures_1.9.28                   
> > [6] AnnotationDbi_1.19.28                    
> > [7] Biobase_2.17.6                           
> > [8] GenomicRanges_1.9.42                     
> > [9] IRanges_1.15.29                          
> > [10] BiocGenerics_0.3.0                       
> 
> > loaded via a namespace (and not attached):
> > [1] biomaRt_2.13.2  bitops_1.0-4.1  BSgenome_1.25.6 DBI_0.2-5      
> > [5] RCurl_1.91-1    RSQLite_0.11.1  stats4_2.15.1   tools_2.15.1   
> > [9] XML_3.9-4       zlibbioc_1.3.0 
-----------------------------------------------------------------------------------------
 

Help much appreciated.
 
Best,
Xiaobei


=
	[[alternative HTML version deleted]]

