Entering edit mode
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/5
1995/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
