Entering edit mode
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