Analysis of peaks generated from Homer using Diffbind
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1
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@gyan-prakash-mishra-8555
Last seen 12 weeks ago
INDIA

Hi,

I have peak file for four different condition without replicate. I converted the text file to Bed file by taking column 2,3,4,8 and 5 which is chr, start, end, score and strand respectively and also removed first 40 line having "#' in the begining. and then created samplesheet "sample.csv" having column Id, tissue, condition, bamreads, bamconrtol, peak, peakcaller.

steps I followed

library(DiffBind)
sample=read.csv("sample.csv")
COR =dba(sampleSheet="sample.csv")

## When i am running below command I am getting error  "Error in pv$peaks[[i]] : subscript out of bounds"

COR = dba.count(COR, minOverlap=3) 
 

1.What is this error?

2.Why I am getting this error ?

3.What is the solution of this?

Thanks in advance.

Gyan Prakash Mishra

diffbind • 1.6k views
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1.) What is the output from traceback(), run right after you get that error?

2.) What is the output for sessionInfo() after you have loaded DiffBind?

 

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Hi James,

Here are the ouputs.

output of sessionInfo()

> sessionInfo()
R Under development (unstable) (2015-07-11 r68646)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

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

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

other attached packages:
 [1] DiffBind_1.14.5         RSQLite_1.0.0           DBI_0.3.1              
 [4] locfit_1.5-9.1          GenomicAlignments_1.4.1 Rsamtools_1.20.4       
 [7] Biostrings_2.36.1       XVector_0.8.0           limma_3.24.14          
[10] GenomicRanges_1.20.5    GenomeInfoDb_1.4.1      IRanges_2.2.5          
[13] S4Vectors_0.6.3         BiocGenerics_0.14.0    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0            lattice_0.20-33        GO.db_3.1.2           
 [4] gtools_3.5.0           digest_0.6.8           plyr_1.8.3            
 [7] futile.options_1.0.0   BatchJobs_1.6          ShortRead_1.26.0      
[10] ggplot2_1.0.1          gplots_2.17.0          zlibbioc_1.14.0       
[13] annotate_1.46.1        gdata_2.17.0           Matrix_1.2-2          
[16] checkmate_1.6.2        systemPipeR_1.2.16     proto_0.3-10          
[19] GOstats_2.34.0         splines_3.3.0          BiocParallel_1.2.9    
[22] stringr_1.0.0          pheatmap_1.0.7         munsell_0.4.2         
[25] sendmailR_1.2-1        base64enc_0.1-3        BBmisc_1.9            
[28] fail_1.2               edgeR_3.10.2           XML_3.98-1.3          
[31] AnnotationForge_1.10.1 MASS_7.3-43            bitops_1.0-6          
[34] grid_3.3.0             RBGL_1.44.0            xtable_1.7-4          
[37] GSEABase_1.30.2        gtable_0.1.2           magrittr_1.5          
[40] scales_0.2.5           graph_1.46.0           KernSmooth_2.23-15    
[43] amap_0.8-14            stringi_0.5-5          hwriter_1.3.2         
[46] reshape2_1.4.1         genefilter_1.50.0      latticeExtra_0.6-26   
[49] futile.logger_1.4.1    brew_1.0-6             rjson_0.2.15          
[52] lambda.r_1.1.7         RColorBrewer_1.1-2     tools_3.3.0           
[55] Biobase_2.28.0         Category_2.34.2        survival_2.38-3       
[58] AnnotationDbi_1.30.1   colorspace_1.2-6       caTools_1.17.1

output of traceback()

> traceback()
4: pv.listadd(peaks, pv$peaks[[i]])
3: pv.vectors(pv, (numpeaks - numAdded + 1):numpeaks, minOverlap = 1,
       bAnalysis = F, bAllSame = T)
2: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,
       bLog = bLog, insertLength = fragmentSize, bOnlyCounts = T,
       bCalledMasks = TRUE, minMaxval = filter, bParallel = bParallel,
       bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl,
       filterFun = filterFun, bLowMem = bUseSummarizeOverlaps, readFormat = readFormat,
       summits = summits, minMappingQuality = mapQCth)
1: dba.count(NCOR1, minOverlap = 3)

 

 

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Entering edit mode
Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 3 days ago
CRUK, Cambridge, UK

I can see the problem in your sample sheet. You have a column named "bamreads" that should be called "bamReads" -- it is case sensitive. Change the column name and see if it works.

Cheers-

Rory

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Hi Rory ,

Thank you so much for help ! I changed 'bamreads" to "bamReads' and Its working.

Regards

Gyan 

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