Plotting the peak counts for filtering
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mc.suciu • 0
@mcsuciu-7753
Last seen 8.9 years ago
United Kingdom

Hi Rory,

I have just recently starting using DiffBind and was hoping you could help me clarify something.

Regarding filtering peaks with few counts, i was wondering if there is a way to plot the distribution of peak counts. I'd like to do this so as to decide what peaks to filter out.

 

Many thanks,

Maria

 

diffbind • 1.1k views
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mc.suciu • 0
@mcsuciu-7753
Last seen 8.9 years ago
United Kingdom

Figured it out, sorry for bothering, it was quite straight forward.

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D'oh, I was just going to answer this one, Glad you figured it out. I assume you know that you can run dba.count() with no filter, then filter by calling dba.count() with peaks=NULL and a value for the filter parameter...

-R

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mc.suciu • 0
@mcsuciu-7753
Last seen 8.9 years ago
United Kingdom

Hi Rory,

Yes, many thanks for replying anyway. I have however ran into another problem. If I have two samples for which I do not have controls. When I try to run the dba. count function with the score as TMM in CPM <test=dba.count(test,minOverlap=2,score=DBA_SCORE_TMM_READS_FULL_CPM)>

I get this error:

<Error in pv.get_reads(pv, g1, bSubControl = bSubControl) : object 'bMinus' not found>

I was wondering if it is possible to get the read count in cpm for the peaks in the samples with no control. I double checked that the sorted bams and their indexes are in the same location, and removed the 'Control' column from sample sheet

Many thanks!

Maria

 

PS: output of sessionInfo()

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

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DESeq2_1.6.2            RcppArmadillo_0.4.500.0
 [3] Rcpp_0.11.3             DESeq_1.18.0           
 [5] lattice_0.20-29         locfit_1.5-9.1         
 [7] Biobase_2.26.0          DiffBind_1.12.3        
 [9] GenomicAlignments_1.2.1 Rsamtools_1.18.2       
[11] Biostrings_2.34.1       XVector_0.6.0          
[13] limma_3.22.1            GenomicRanges_1.18.3   
[15] GenomeInfoDb_1.2.5      IRanges_2.0.1          
[17] S4Vectors_0.4.0         BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      amap_0.8-12          annotate_1.44.0     
 [4] AnnotationDbi_1.28.1 base64enc_0.1-2      BatchJobs_1.5       
 [7] BBmisc_1.8           BiocParallel_1.0.0   bitops_1.0-6        
[10] brew_1.0-6           caTools_1.17.1       checkmate_1.5.1     
[13] cluster_1.15.3       codetools_0.2-9      colorspace_1.2-4    
[16] DBI_0.3.1            digest_0.6.6         edgeR_3.8.5         
[19] fail_1.2             foreach_1.4.2        foreign_0.8-61      
[22] Formula_1.1-2        gdata_2.13.3         genefilter_1.48.1   
[25] geneplotter_1.44.0   ggplot2_1.0.0        gplots_2.15.0       
[28] grid_3.1.1           gtable_0.1.2         gtools_3.4.1        
[31] Hmisc_3.14-6         iterators_1.0.7      KernSmooth_2.23-13  
[34] latticeExtra_0.6-26  MASS_7.3-35          munsell_0.4.2       
[37] nnet_7.3-8           plyr_1.8.1           proto_0.3-10        
[40] RColorBrewer_1.1-2   reshape2_1.4.1       rpart_4.1-8         
[43] RSQLite_1.0.0        scales_0.2.4         sendmailR_1.2-1     
[46] splines_3.1.1        stringr_0.6.2        survival_2.37-7     
[49] tools_3.1.1          XML_3.98-1.1         xtable_1.7-4        
[52] zlibbioc_1.12.0 

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Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK

Hi Maria-

You have discovered a bug. I have checked in a fix. It will appear in DiffBind 1.14.4 in the next day or two. To get this fix, you'll need to be on Bioconductor 3.1, which runs on R 3.2.0.

-Rory

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