[BioC] Rsubread featureCounts question

[Wei Shi]

Dear Jim,

We found a bug in the C code which seemed to cause the problems you have encountered. We are now investigating this and will come up with a fix for them in the next few days. 

Thanks,
Wei

On Oct 23, 2013, at 8:21 AM, James W. MacDonald wrote:

> I am confused by this output from featureCounts():
> 
> > dat1 <- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE)
> > head(dat1$annotation)
>     GeneID  Chr   Start     End Strand Length
> 1    497097 chr1 3214482 3216968      -   2487
> 2    497097 chr1 3421702 3421901      -    200
> 3    497097 chr1 3670552 3671498      -    947
> 4 100503874 chr1 3647309 3650509      -   3201
> 5 100503874 chr1 3658847 3658904      -     58
> 6 100038431 chr1 3680155 3681788      +   1634
> > head(dat1$counts)
>          [,1]
> 497097       0
> 497097       0
> 497097       0
> 100503874    0
> 100503874    0
> 100038431    0
> 
> The help page indicates that this should result in output that has been aggregated over each gene, not each exon.
> 
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
> 
> other attached packages:
> [1] affycoretools_1.34.0 KEGG.db_2.10.1       GO.db_2.10.1
> [4] affy_1.40.0          ReportingTools_2.2.0 knitr_1.5
> [7] edgeR_3.4.0          limma_3.18.0         org.Mm.eg.db_2.10.1
> [10] RSQLite_0.11.4       DBI_0.2-7            AnnotationDbi_1.24.0
> [13] Biobase_2.22.0       BiocGenerics_0.8.0   Rsubread_1.12.0
> [16] BiocInstaller_1.12.0
> 
> Best,
> 
> Jim
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
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