generate RangedData from DiffBind
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@joydeepbhadury-6860
Last seen 7.6 years ago
Sweden

Hi

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

I tried
dba.report(DBA, 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 • 1.2k views
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Hi,

I can't reproduce this.  When I try:

> rep = dba.report(analysis,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()"?

Thanks,

 - Gord

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

locale:
[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       

 

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

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@joydeepbhadury-6860
Last seen 7.6 years ago
Sweden

Hi

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 :-)

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