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Question: Analysis of peaks generated from Homer using Diffbind
0
gravatar for Gyan Prakash Mishra
3.2 years ago by
INDIA
Gyan Prakash Mishra0 wrote:

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

ADD COMMENTlink modified 3.2 years ago by Rory Stark2.6k • written 3.2 years ago by Gyan Prakash Mishra0

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?

 

ADD REPLYlink written 3.2 years ago by James W. MacDonald48k

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)

 

 

ADD REPLYlink written 3.2 years ago by Gyan Prakash Mishra0
1
gravatar for Rory Stark
3.2 years ago by
Rory Stark2.6k
CRUK, Cambridge, UK
Rory Stark2.6k wrote:

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

ADD COMMENTlink written 3.2 years ago by Rory Stark2.6k

Hi Rory ,

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

Regards

Gyan 

ADD REPLYlink written 3.2 years ago by Gyan Prakash Mishra0
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