Question: generate RangedData from DiffBind
gravatar for joydeepbhadury
5.1 years ago by
joydeepbhadury0 wrote:


i would like to get help to export my data from diffbind into ChIPPeakAnno for annotation

I tried, contrast=1, bNormalized=TRUE,bCalled=FALSE, bCounts=FALSE, bCalledDetail=FALSE,bAll=TRUE,file="test",ext="csv",DataType=DBA_DATA_RANGEDDATA)               

but the output is not recognized by ChIPPeakAnno as an input..




chippeakanno diffbind • 943 views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by joydeepbhadury0


I can't reproduce this.  When I try:

> rep =,contrast=1, bNormalized=TRUE,bCalled=FALSE, bCounts=FALSE, bCalledDetail=FALSE,bAll=TRUE,file="test",ext="csv",DataType=DBA_DATA_RANGEDDATA)

followed by

> library(biomaRt)
> library(ChIPpeakAnno)
> m = useMart('ensembl')
> m = useDataset('hsapiens_gene_ensembl',m)
> a = annotatePeakInBatch(rep,mart=m,featureType = c("TSS") )

I get annotations successfully.   Can you provide more specific information regarding what you tried, and what the error message was, including the output of "sessionInfo()"?


 - Gord

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

[1] C

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

other attached packages:
 [1] ChIPpeakAnno_2.16.0       AnnotationDbi_1.28.1     
 [3] RSQLite_1.0.0             DBI_0.3.1                
 [5] biomaRt_2.22.0            VennDiagram_1.6.9        
 [7] DESeq2_1.6.1              RcppArmadillo_0.4.450.1.0
 [9] Rcpp_0.11.3               DESeq_1.18.0             
[11] lattice_0.20-29           locfit_1.5-9.1           
[13] Biobase_2.26.0            DiffBind_1.12.0          
[15] GenomicAlignments_1.2.0   Rsamtools_1.18.1         
[17] Biostrings_2.34.0         XVector_0.6.0            
[19] limma_3.22.1              GenomicRanges_1.18.1     
[21] GenomeInfoDb_1.2.2        IRanges_2.0.0            
[23] S4Vectors_0.4.0           BiocGenerics_0.12.0      

loaded via a namespace (and not attached):
 [1] BBmisc_1.7             BSgenome_1.34.0        BatchJobs_1.4         
 [4] BiocParallel_1.0.0     Formula_1.1-2          GO.db_3.0.0           
 [7] GenomicFeatures_1.18.2 Hmisc_3.14-5           KernSmooth_2.23-13    
[10] MASS_7.3-35            RColorBrewer_1.0-5     RCurl_1.95-4.3        
[13] XML_3.98-1.1           acepack_1.3-3.3        amap_0.8-12           
[16] annotate_1.44.0        base64enc_0.1-2        bitops_1.0-6          
[19] brew_1.0-6             caTools_1.17.1         checkmate_1.5.0       
[22] cluster_1.15.3         codetools_0.2-9        colorspace_1.2-4      
[25] digest_0.6.4           edgeR_3.8.2            fail_1.2              
[28] foreach_1.4.2          foreign_0.8-61         gdata_2.13.3          
[31] genefilter_1.48.1      geneplotter_1.44.0     ggplot2_1.0.0         
[34] gplots_2.14.2          gtable_0.1.2           gtools_3.4.1          
[37] iterators_1.0.7        latticeExtra_0.6-26    multtest_2.22.0       
[40] munsell_0.4.2          nnet_7.3-8             plyr_1.8.1            
[43] proto_0.3-10           reshape2_1.4           rpart_4.1-8           
[46] rtracklayer_1.26.1     scales_0.2.4           sendmailR_1.2-1       
[49] splines_3.1.1          stringr_0.6.2          survival_2.37-7       
[52] tools_3.1.1            xtable_1.7-4           zlibbioc_1.12.0       


ADD REPLYlink written 5.1 years ago by Gord Brown590

Hi @GordBrown How can I modify these lines of code to get my annotation in terms of HGNC

ADD REPLYlink modified 6 months ago • written 6 months ago by researcher0
Answer: generate RangedData from DiffBind
gravatar for joydeepbhadury
5.1 years ago by
joydeepbhadury0 wrote:


Thanks for the reply. I did exactly what i had posted here and as you mentioned its working now. I have no clue why but thanks a lot :-)

ADD COMMENTlink written 5.1 years ago by joydeepbhadury0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 323 users visited in the last hour