[BioC] Rsubread featureCounts question

[James W. MacDonald]

Thanks Wei!

On Friday, October 25, 2013 8:18:44 AM, Wei Shi wrote:
> Dear Jim,
>
> We have fixed the problems you have encountered and committed the changes to the release version of Rsubread (1.12.1). It should be available in a couple of days.
>
> Best regards,
> 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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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099