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  • Rapidr invalid class “SummarizedExperiment”

    Hello everybody,

    I am trying to set up a pipeline to aneuploidy prenatal diagnostic. In order to perform the analysis, I am using rapidR.

    To create a binned bound file from BAM's, I do;

    makeBinnedCountsFile(bam.file.list = c("trisomie_sorted.bam"),sampleIDs = c("SRR611850"), binned.counts.fname = output.fname, k = 20000)

    first would like to know what is the parameter ki, at the manual it is defined ask is the bin size, default is 20000 kb, is it the size of the bam file (binary) in kb?

    When I execute the command above I got the following error:

    > makeBinnedCountsFile(bam.file.list = c("trisomie_sorted.bam"),sampleIDs = c("SRR611850"), binned.counts.fname = output.fname, k = 20000)
    Binning counts in bam files
    doing the binning
    Error in validObject(.Object) :
    invalid class “SummarizedExperiment” object: 'rowRanges' length differs from 'assays' nrow

    Can anybody tell me how to deal with it? There is some tutorial (with bam files included) to learn how to use RapidR?

    thanks


    > sessionInfo()
    R version 3.2.2 (2015-08-14)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 14.04.3 LTS

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

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

    other attached packages:
    [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.3
    [3] rtracklayer_1.28.10 Biostrings_2.36.4
    [5] XVector_0.8.0 GenomicRanges_1.20.6
    [7] GenomeInfoDb_1.4.2 IRanges_2.2.7
    [9] S4Vectors_0.6.5 BiocGenerics_0.14.0
    [11] RAPIDR_0.1.1

    loaded via a namespace (and not attached):
    [1] Rcpp_0.12.1 magrittr_1.5 zlibbioc_1.14.0
    [4] GenomicAlignments_1.4.1 BiocParallel_1.2.21 stringr_1.0.0
    [7] plyr_1.8.3 tools_3.2.2 data.table_1.9.4
    [10] lambda.r_1.1.7 futile.logger_1.4.1 reshape2_1.4.1
    [13] PropCIs_0.2-5 futile.options_1.0.0 bitops_1.0-6
    [16] RCurl_1.95-4.7 stringi_0.5-5 Rsamtools_1.20.4
    [19] XML_3.98-1.3 chron_2.3-47
    >

  • #2
    Rapidr

    Hi,
    Use this command
    makeBinnedCountsFile(c("trisomie_sorted.bam"), c("SRR611850"), 'output.fname', k = 20000)
    Before running the command please index bam file and keep the index(.bai)
    in the same folder.

    Comment


    • #3
      thanks for your help

      pau

      Comment


      • #4
        Hi,
        I think this is very late in this discussion!
        I am confused that, our reference set should be of known samples, which requires normal as well as abnormal samples?

        Comment

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