[BioC] Rsubread featureCounts question

[James W. MacDonald]

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