Hi,
I have been using DESeq2 and reporting tools for quite some time. I have used the [ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids from this post to use ensembl gene IDs to get Biomart information. I have attached the code I have been using to find that most of the ID's map to a proper gene symbol and GO id with an image, log change and p-value. But for some ID's , although I know which gene ID they belong to based on the graph's annotation, it is not getting displayed in the HTML report. I am not able to understand why if most the genes can be listed in the report, when some of them alone cannot be?
Here is my R code:
#Run the Reporting Tools
library (biomaRt)
library(ReportingTools)
mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl")
add.anns <- function(df, mart, ...)
{
nm <- rownames(df)
anns <- getBM(attributes = c("ensembl_gene_id","external_gene_name", "description","go_id","name_1006"),
filters = "ensembl_gene_id", values = nm, mart = mart)
anns <- anns[match(nm, anns[, 1]), ]
colnames(anns) <- c("ID", "Gene Symbol", "Gene Description", "GO Term Accession", "GO Term Name")
#colnames(anns) <- c("ID", "Gene Symbol")
df <- cbind(anns, df[, 2:ncol(df)])
#df <- cbind(anns, df[,-1])
rownames(df) <- nm
df
}
htmlReport <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq2',title = 'RNA-seq analysis of differential expression using DESeq2',
reportDirectory = "./report")
publish (dds, factor= colData(dds)$condition, htmlReport, reportDir="./report", .modifyDF = list(add.anns, modifyReportDF), mart = mart )
#publish (res, htmlReport, reportDir="./report", mart = mart )
finish(htmlReport)
Here is the R session.
> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)
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 stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.26.1 BiocInstaller_1.20.1 RColorBrewer_1.1-2 gplots_3.0.1
[5] ReportingTools_2.10.0 knitr_1.12.3 org.Mm.eg.db_3.2.3 RSQLite_1.0.0
[9] DBI_0.3.1 AnnotationDbi_1.32.3 calibrate_1.7.2 MASS_7.3-45
[13] DESeq2_1.10.1 RcppArmadillo_0.6.700.3.0 Rcpp_0.12.4 SummarizedExperiment_1.0.2
[17] Biobase_2.30.0 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8
[21] S4Vectors_0.8.11 BiocGenerics_0.16.1
