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Question: Error in binning bam files
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gravatar for greeshmathulasi1
9 months ago by
greeshmathulasi10 wrote:

Hi everyone,

while running code,

> makeBinnedCountsFile(bam.file.list = c("sample5.bam", "sample6.bam"),
+                       sampleIDs = c("", ""),
+                       binned.counts.fname = output.fname,
+                       k = 20000, mask)

I am getting error msg as: Binning counts in bam files
doing the binning
Error in assays(olap) : could not find function "assays"

The sessioninfo is:

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] RAPIDR_0.1.1                      GenomeInfoDbData_0.99.0          
 [3] matrixStats_0.52.2                Biobase_2.36.2                   
 [5] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.44.2                  
 [7] rtracklayer_1.36.6                Biostrings_2.44.2                
 [9] XVector_0.16.0                    GenomicRanges_1.28.6             
[11] GenomeInfoDb_1.12.3               IRanges_2.10.5                   
[13] S4Vectors_0.14.7                  BiocGenerics_0.22.1              
[15] BiocInstaller_1.26.1             

loaded via a namespace (and not attached):
 [1] zlibbioc_1.22.0            GenomicAlignments_1.12.2   BiocParallel_1.10.1       
 [4] lattice_0.20-35            tools_3.4.2                SummarizedExperiment_1.6.5
 [7] grid_3.4.2                 data.table_1.10.4-1        Matrix_1.2-11             
[10] PropCIs_0.2-5              bitops_1.0-6               RCurl_1.95-4.8            
[13] DelayedArray_0.3.21        compiler_3.4.2             Rsamtools_1.28.0          
[16] XML_3.98-1.9 

ADD COMMENTlink modified 9 months ago • written 9 months ago by greeshmathulasi10
0
gravatar for Martin Morgan
9 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

RAPIDR (I think that's the package defining makeBinnedCountsFile ?) is not a Bioconductor package, so you would rather contact maintainer("RAPIDR"). It looks like the package author did not formulate their NAMESPACE correctly; try evaluating

library(SummarizedExperiment)

before the code chunk above.

ADD COMMENTlink written 9 months ago by Martin Morgan ♦♦ 22k
0
gravatar for greeshmathulasi1
9 months ago by
greeshmathulasi10 wrote:

Yes. There are dependency problems among RAPIDR packages like S4vectors, SummarizedExperiment etc. If one's version is updated, then the other will be incompatible.

ADD COMMENTlink written 9 months ago by greeshmathulasi10
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