Question: RIPSeeker error regarding binSize, only for control samples
0
gravatar for fitzgeraldd424
18 months ago by
fitzgeraldd4240 wrote:

Hi, 

I'm trying to use RIPseeker to to analyze some data (not RIP-seq, but expect similar one-stranded peaks). I can load my data in, generate plots in RIPSeeker (with plotStrandedCoverage), and run the ripSeek command without a control file. However, when I try to run ripSeek with a control file included (input control), I get the following error: "Error in sprintf("***0. Using predefined binSize of %d bp.", binSize) : unsupported type". The error happens regardless of whether I provide a binSize or calculate one within the ripSeek command and is independent of the file assigned as control (can assign a file that works as a RIP file as the control and get the same error). Please help!

Thanks,

Devon

R code:

bamFiles <- c("test1.bam", "test2.bam", "input.bam")

cNAME <- "input"

outDir <- file.path(getwd(), "RIPSeeker_test")

binSize <- NULL      # set to NULL to automatically determine bin size

minBinSize <- 50  # min bin size in automatic bin size selection

maxBinSize <- 500 # max bin size in automatic bin size selection

multicore <- TRUE # use multicore

strandType <- "+" # set strand type to minus strand

 

seekOut.TEST.plus <- ripSeek(bamPath = bamFiles, cNAME = cNAME,

                   reverseComplement = TRUE,

                   strandType = strandType, paired = TRUE,

                   uniqueHit = TRUE, assignMultihits = TRUE,

                   rerunWithDisambiguatedMultihits = TRUE,

                   binSize=binSize)

 

Full output:

*I. Collect alignment files

 

 

RIP alignment files:

test1.bam

test2.bam

 

 

Control alignment files:

input.bam

 

 

 

*II. Analyzing RIP library:

 

 

**A. Process and combine alignment files

 

Processing test1.bam ... GAlignments object contains 114 out-of-bound ranges located on sequence chr1. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not

  considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences).115 read-pairs with end larger than chromosome length are discardedAll hits are returned with flags.

Processing test2.bam ... GAlignments object contains 40 out-of-bound ranges located on sequence chr1. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not

  considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences).41 read-pairs with end larger than chromosome length are discardedAll hits are returned with flags.

2 BAM files are combined

* Only reads from strand + will be considered.

* Only unique hits are used to compute read count.

* All chromosomes have at least one alignment

 

**B. Run NB HMM on each chromosome

 

 


chr1:


 

 

*0. Computing optimal bin size.

 

Optimal bin size: 200 bp

 

*1. Traning NB HMM to derive posterior (and Viterbi state sequence:)

 

*1. Initializing negative binomial HMM (nbh) with 2 states:

 

 

Starting NB mixture model (nbm_em) for K=2 clusters:

Iteration 0: -201609.663

Iteration 1: -176794.357

Iteration 2: -171303.981

Iteration 3: -165668.298

Iteration 4: -158963.471

Iteration 5: -153561.867

Iteration 6: -148361.207

Iteration 7: -143409.767

Iteration 8: -138773.494

Iteration 9: -134508.689

Iteration 10: -130658.151

Iteration 11: -127248.477

Iteration 12: -124298.263

Iteration 13: -121838.340

Iteration 14: -119587.219

Iteration 15: -117634.789

Iteration 16: -116229.736

Iteration 17: -115124.218

 

*2. Traininig nbh with forward-backward algorithm:

 

Iteration 0: -114272.347

Iteration 1: -113628.000

Iteration 2: -113150.942

Iteration 3: -112805.237

Iteration 4: -112560.435

Iteration 5: -112391.531

Iteration 6: -112278.560

Iteration 7: -112205.970

 

*3. Deriving maximum-likelihood hidden state sequence with Viterbi algorithm:

 

done!

 

 

*II.2. Analyzing control library:

 

 

**A. Process and combine alignment files

 

Processing input.bam ... GAlignments object contains 28 out-of-bound ranges located on sequence chr1. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not

  considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences).29 read-pairs with end larger than chromosome length are discardedAll hits are returned with flags.

1 BAM files are combined

* Only reads from strand + will be considered.

* Only unique hits are used to compute read count.

* All chromosomes have at least one alignment

 

**B. Run NB HMM on each chromosome

 

 


chr1:


 

Error in sprintf("*0. Using predefined binSize of %d bp.", binSize) : 

  unsupported type

 

Session info:

> sessionInfo()

R version 3.5.0 (2018-04-23)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: OS X El Capitan 10.11.6

Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

 [1] ChIPpeakAnno_3.14.0         VennDiagram_1.6.20          futile.logger_1.4.3         RIPSeekerData_1.16.0        RIPSeeker_1.20.0            rtracklayer_1.40.2          biomaRt_2.36.0             

 [8] BiocInstaller_1.30.0        ggbio_1.28.0                GenomicAlignments_1.16.0    SummarizedExperiment_1.10.1 DelayedArray_0.6.0          BiocParallel_1.14.1         matrixStats_0.53.1         

[15] Biobase_2.40.0              Rsamtools_1.32.0            Biostrings_2.48.0           XVector_0.20.0              ggplot2_2.2.1               hiAnnotator_1.14.0          Gviz_1.24.0                

[22] GenomicRanges_1.32.3        GenomeInfoDb_1.16.0         IRanges_2.14.10             S4Vectors_0.18.2            BiocGenerics_0.26.0        

loaded via a namespace (and not attached):

 [1] nlme_3.1-137             ProtGenerics_1.12.0      bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2       progress_1.1.2           httr_1.3.1               tools_3.5.0             

 [9] backports_1.1.2          R6_2.2.2                 rpart_4.1-13             mgcv_1.8-23              Hmisc_4.1-1              DBI_1.0.0                lazyeval_0.2.1           colorspace_1.3-2        

[17] ade4_1.7-11              nnet_7.3-12              gridExtra_2.3            prettyunits_1.0.2        GGally_1.3.2             bit_1.1-13               curl_3.2                 compiler_3.5.0          

[25] graph_1.58.0             formatR_1.5              htmlTable_1.11.2         labeling_0.3             scales_0.5.0             checkmate_1.8.5          RBGL_1.56.0              stringr_1.3.1           

[33] digest_0.6.15            foreign_0.8-70           pkgconfig_2.0.1          base64enc_0.1-3          dichromat_2.0-0          htmltools_0.3.6          regioneR_1.12.0          limma_3.36.1            

[41] ensembldb_2.4.1          BSgenome_1.48.0          htmlwidgets_1.2          rlang_0.2.0              rstudioapi_0.7           RSQLite_2.1.1            bindr_0.1.1              acepack_1.4.1           

[49] dplyr_0.7.4              VariantAnnotation_1.26.0 RCurl_1.95-4.10          magrittr_1.5             GO.db_3.6.0              GenomeInfoDbData_1.1.0   Formula_1.2-3            Matrix_1.2-14           

[57] Rcpp_0.12.16             munsell_0.4.3            stringi_1.2.2            yaml_2.1.19              MASS_7.3-50              zlibbioc_1.26.0          plyr_1.8.4               blob_1.1.1              

[65] lattice_0.20-35          splines_3.5.0            multtest_2.36.0          GenomicFeatures_1.32.0   knitr_1.20               pillar_1.2.2             seqinr_3.4-5             reshape2_1.4.3          

[73] codetools_0.2-15         futile.options_1.0.1     glue_1.2.0               XML_3.98-1.11            biovizBase_1.28.0        latticeExtra_0.6-28      lambda.r_1.2.2           data.table_1.11.2       

[81] idr_1.2                  foreach_1.4.4            gtable_0.2.0             reshape_0.8.7            assertthat_0.2.0         AnnotationFilter_1.4.0   survival_2.42-3          tibble_1.4.2            

[89] OrganismDbi_1.22.0       iterators_1.0.9          AnnotationDbi_1.42.1     memoise_1.1.0            bindrcpp_0.2.2           cluster_2.0.7-1     

ripseeker • 221 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by fitzgeraldd4240
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