Error with Reportingtools using ENSEMBL gene ID
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cagenet34 ▴ 20
@cagenet34-10910
Last seen 3.2 years ago
Toulouse, France, INRA

Dear all,

I'm using ReportingTools with DESeq 2. I'm working with Ensembl Gene ID, for this I'm using recommendation on previous posts her (i.e. create a function). After several error, I have to use R-3.3.1 because of  problem with "survival" .

At the end of Reportingtools, I obtained no error but I only have in the table results the ensembl gene ID (no hgnc, no description).

Any help will be really appreciate, Thanks in advance,

You will find below my script.

rm(list=ls())  
workDir <- "C:/Users/cagenet/Documents/AMHAROC/3_Analyses_bioinfo/Analyse_Stat"
setwd(workDir)
AMHdup<-read.csv(file="count_genes_8indi_RmDup.csv", sep = ";",header=TRUE,row.names=1 )
dim(AMHdup)
library(DESeq2)
#HTSFilter
library(HTSFilter)
coldatafile<-read.table(file="colData.txt",sep="\t",header=TRUE,row.names=1)
colnames(AMHdup) <- NULL # pour éviter l'erreur avec summarizedExperiment
dds<-DESeqDataSetFromMatrix(countData = AMHdup,
                            colData = coldatafile,
                            design = ~ Treatment)
dds <-dds[rowSums(counts(dds)) > 1,] ##  minimal pre-filtering en virant les lignes avec 0 ou 1 reads.
nrow(dds)
dds1<-dds
dds1<-DESeq(dds1) # on lance l'analyse différentielle
filterHTS<-HTSFilter(dds1,s.len=500, plot=TRUE)$filteredData
dim(filterHTS) # on réduit à 12800
res<-results(filterHTS, independentFiltering = FALSE) ## on utilise les 12700 gènes ayant passé le seuil et on continue avec DESEQ2
library(ReportingTools)
library(biomaRt)
ensembl<-useEnsembl(biomart="ensembl",dataset="oaries_gene_ensembl")# use ensembl host
#creating function to work with ensembl gene ID as input
add.anns <- function (dds1, ensembl, ...)
{
  nm <- rownames(dds1)
  anns <- getBM(
    attributes = c("ensembl_gene_id","hgnc_symbol", "description"),
    filters = "ensembl_gene_id", values = nm, mart = ensembl)
  anns <- anns[match(nm, anns[, 1]), ]
  colnames(anns) <- c("ID", "Gene Symbol", "Gene Description")
  dds1 <- cbind (anns, dds1[,-1, drop=FALSE])
  rownames(dds1) <- nm
  dds1
}
des2Report <- HTMLReport(shortName = 'RNAseq_analysis_with_DESeq2',
                         title = 'RNA-seq analysis of differential expression using DESeq2',
                         reportDirectory = "./reports")
publish(dds1,des2Report, pvalueCutoff=0.05,
       factor = colData(dds1)$Treatment,
        modifyDF=list(add.anns, modifyReportDF),
        reportDirectory="./reports")
finish(des2Report)

 

> sessionInfo(package = NULL)
R version 3.3.1 RC (2016-06-17 r70798)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.28.0             ReportingTools_2.12.2      BiocInstaller_1.22.2      
 [4] knitr_1.13                 DESeq2_1.12.3              SummarizedExperiment_1.2.3
 [7] Biobase_2.32.0             GenomicRanges_1.24.1       GenomeInfoDb_1.8.2        
[10] IRanges_2.6.0              S4Vectors_0.10.1           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] httr_1.2.0                    edgeR_3.14.0                 
 [3] AnnotationHub_2.4.2           splines_3.3.1                
 [5] R.utils_2.3.0                 Formula_1.2-1                
 [7] shiny_0.13.2                  interactiveDisplayBase_1.10.3
 [9] latticeExtra_0.6-28           RBGL_1.48.1                  
[11] BSgenome_1.40.1               Rsamtools_1.24.0             
[13] Category_2.38.0               RSQLite_1.0.0                
[15] lattice_0.20-33               biovizBase_1.20.0            
[17] limma_3.28.6                  chron_2.3-47                 
[19] digest_0.6.9                  RColorBrewer_1.1-2           
[21] XVector_0.12.0                colorspace_1.2-6             
[23] ggbio_1.20.1                  R.oo_1.20.0                  
[25] httpuv_1.3.3                  htmltools_0.3.5              
[27] Matrix_1.2-6                  plyr_1.8.4                   
[29] OrganismDbi_1.14.1            GSEABase_1.34.0              
[31] XML_3.98-1.4                  genefilter_1.54.2            
[33] zlibbioc_1.18.0               xtable_1.8-2                 
[35] GO.db_3.3.0                   scales_0.4.0                 
[37] BiocParallel_1.6.2            annotate_1.50.0              
[39] ggplot2_2.1.0                 PFAM.db_3.3.0                
[41] GenomicFeatures_1.24.2        nnet_7.3-12                  
[43] mime_0.4                      survival_2.39-4              
[45] magrittr_1.5                  R.methodsS3_1.7.1            
[47] GGally_1.1.0                  hwriter_1.3.2                
[49] foreign_0.8-66                GOstats_2.38.0               
[51] graph_1.50.0                  tools_3.3.1                  
[53] data.table_1.9.6              stringr_1.0.0                
[55] munsell_0.4.3                 locfit_1.5-9.1               
[57] cluster_2.0.4                 AnnotationDbi_1.34.3         
[59] ensembldb_1.4.6               Biostrings_2.40.2            
[61] grid_3.3.1                    RCurl_1.95-4.8               
[63] dichromat_2.0-0               VariantAnnotation_1.18.1     
[65] AnnotationForge_1.14.2        bitops_1.0-6                 
[67] gtable_0.2.0                  DBI_0.4-1                    
[69] reshape_0.8.5                 reshape2_1.4.1               
[71] R6_2.1.2                      GenomicAlignments_1.8.1      
[73] gridExtra_2.2.1               rtracklayer_1.32.0           
[75] Hmisc_3.17-4                  stringi_1.1.1                
[77] Rcpp_0.12.5                   geneplotter_1.50.0           
[79] rpart_4.1-10                  acepack_1.3-3.3              
>

 

 

reporting tools modifyDF survival • 967 views
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