[BioC] ReportingTools and gene annotation

[Ugo Borello]

Good morning,
I am using ReportingTools with DESeq2 and I am not able to add the gene
annotation to my final report.
I have ensembl gene id as identifiers and not entrez id!

I followed Jason's suggestions as described here:

http://article.gmane.org/gmane.science.biology.informatics.conductor/51995/m
atch=

But the add.anns() functions doesn't work in my hands.

> mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl")

> add.anns <- function(df, mart, ...)
+ {
+   nm <- rownames(df)
+   anns <- getBM(
+     attributes = c("ensembl_gene_id", "external_gene_id", "description"),
+     filters = "ensembl_gene_id", values = nm, mart = mart)
+   anns <- anns[match(nm, anns[, 1]), ]
+   colnames(anns) <- c("ID", "Gene Symbol", "Gene Description")
+   df <- cbind(anns, df[, 2:nrow(df)])
+   rownames(df) <- nm
+   df
+ }
> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF =
list(add.anns, modifyReportDF), mart = mart)    ## dds is the DESeqDataSet
object

 Show Traceback
 Rerun with Debug
 Error in `[.data.frame`(df, , 2:nrow(df)) : undefined columns selected

I also tried this:
> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF =
list(add.anns, modifyReportDF), mart = mart, df= counts(dds))  # dds is the
DESeqDataSet object

 Show Traceback
 Rerun with Debug
 Error in df[, 2:nrow(df)] : subscript out of bounds


What am I doing wrong?

Is there a simple way of adding my annotation to the HTML report?

 ENSEMBL                          ENTREZID SYMBOL     GENENAME
1 ENSMUSG00000000001    14679   Gnai     guanine nucleotide binding protein
(G protein), alpha inhibiting 3
2 ENSMUSG00000000028    12544  Cdc45   cell division cycle 45
3 ENSMUSG00000000031       NA     NA      NA
4 ENSMUSG00000000037   107815  Scml2  sex comb on midleg-like 2 (Drosophila)
5 ENSMUSG00000000049    11818   Apoh    apolipoprotein H
6 ENSMUSG00000000056    67608   Narf     nuclear prelamin A recognition
factor


Thank you

Ugo


> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
 [1] ReportingTools_2.2.0    knitr_1.5               org.Mm.eg.db_2.10.1
RSQLite_0.11.4          DBI_0.2-7
 [6] AnnotationDbi_1.24.0    Biobase_2.22.0          DESeq2_1.2.9
RcppArmadillo_0.4.000.2 Rcpp_0.10.6
[11] GenomicRanges_1.14.4    XVector_0.2.0           IRanges_1.20.6
BiocGenerics_0.8.0      biomaRt_2.18.0

loaded via a namespace (and not attached):
 [1] annotate_1.40.0          AnnotationForge_1.4.4    Biostrings_2.30.1
biovizBase_1.10.7        bitops_1.0-6
 [6] BSgenome_1.30.0          Category_2.28.0          cluster_1.14.4
colorspace_1.2-4         dichromat_2.0-0
[11] digest_0.6.4             edgeR_3.4.2              evaluate_0.5.1
formatR_0.10             Formula_1.1-1
[16] genefilter_1.44.0        GenomicFeatures_1.14.2   ggbio_1.10.10
ggplot2_0.9.3.1          GO.db_2.10.1
[21] GOstats_2.28.0           graph_1.40.1             grid_3.0.2
gridExtra_0.9.1          GSEABase_1.24.0
[26] gtable_0.1.2             Hmisc_3.14-0             hwriter_1.3
labeling_0.2             lattice_0.20-24
[31] latticeExtra_0.6-26      limma_3.18.10            locfit_1.5-9.1
MASS_7.3-29              Matrix_1.1-2
[36] munsell_0.4.2            PFAM.db_2.10.1           plyr_1.8
proto_0.3-10             R.methodsS3_1.6.1
[41] R.oo_1.17.0              R.utils_1.28.4           RBGL_1.38.0
RColorBrewer_1.0-5       RCurl_1.95-4.1
[46] reshape2_1.2.2           Rsamtools_1.14.2         rtracklayer_1.22.3
scales_0.2.3             splines_3.0.2
[51] stats4_3.0.2             stringr_0.6.2            survival_2.37-7
tools_3.0.2              VariantAnnotation_1.8.10
[56] XML_3.95-0.2             xtable_1.7-1             zlibbioc_1.8.0