Question: Error with Reportingtools using ENSEMBL gene ID
0
gravatar for cagenet34
2.8 years ago by
cagenet3420
Toulouse, France, INRA
cagenet3420 wrote:

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              
>

 

 

ADD COMMENTlink written 2.8 years ago by cagenet3420
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