Question: ASpli AsDiscover error
0
gravatar for abdul rawoof
10 months ago by
abdul rawoof60
United States
abdul rawoof60 wrote:

Hello everyone,

I am performing alternative splicing analysis in my transcriptome samples using ASpli R package.
However, while performing analysis using function AsDiscover I got following error
#######################
>AsDiscover(counts = counts, targets = targets, features = features, bam = bam1, l=100L, threshold = 10,cores = 10,pair = pair)

Error in data.frame(matrix(unlist(strsplit(jnames, "[.]")), byrow = TRUE,  :
row names supplied are of the wrong length

#######################

I checked row length for gene.counts in counts object and genes in features object. And both are having same row length. Anyone can point out which step I should work on to get rid of this error ????
Here is the session info in R

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_IN.UTF-8    LC_NUMERIC=C    LC_TIME=en_IN.UTF-8    LC_COLLATE=en_IN.UTF-8    LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8    LC_NAME=C    LC_ADDRESS=C    LC_TELEPHONE=C     LC_MEASUREMENT=en_IN.UTF-8    LC_IDENTIFICATION=C       

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

other attached packages:
 [1] dMod_0.4.2     cOde_0.4.1     GenomicFeatures_1.28.0 AnnotationDbi_1.38.2   Biobase_2.36.2    GenomicRanges_1.28.6   GenomeInfoDb_1.12.3   
 [8] ASpli_1.2.4    Biostrings_2.44.2      XVector_0.16.0    IRanges_2.10.5    S4Vectors_0.14.7       BiocGenerics_0.22.1   

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.8.0    bitops_1.0-6    matrixStats_0.52.2    RColorBrewer_1.1-2    httr_1.4.0
 [6] tools_3.4.2    backports_1.1.3    R6_2.3.0    rpart_4.1-11    Hmisc_4.1-1
[11] DBI_0.7        lazyeval_0.2.1     Gviz_1.20.0    colorspace_1.3-2      nnet_7.3-12
[16] tidyselect_0.2.5      gridExtra_2.3    DESeq2_1.16.1    curl_3.2    compiler_3.4.2
[21] htmlTable_1.12     DelayedArray_0.2.7    rtracklayer_1.36.6    scales_1.0.0    checkmate_1.8.5
[26] genefilter_1.58.1     stringr_1.3.1    digest_0.6.18    Rsamtools_1.28.0      foreign_0.8-69
[31] base64enc_0.1-3    dichromat_2.0-0    pkgconfig_2.0.2    htmltools_0.3.6    ensembldb_2.0.4
[36] limma_3.32.10    BSgenome_1.42.0    htmlwidgets_1.3    rlang_0.3.0.1    rstudioapi_0.8
[41] RSQLite_1.1-2    BiocInstaller_1.26.1    shiny_1.0.0    bindr_0.1.1    DEXSeq_1.22.0
[46] hwriter_1.3.2    BiocParallel_1.10.1    acepack_1.4.1    dplyr_0.7.7    VariantAnnotation_1.22.3
[51] RCurl_1.95-4.11    magrittr_1.5    GenomeInfoDbData_0.99.0       Formula_1.2-3    Matrix_1.2-11
[56] Rcpp_1.0.0    munsell_0.5.0    stringi_1.2.4    yaml_2.2.0    edgeR_3.18.1
[61] rootSolve_1.7    SummarizedExperiment_1.6.5    zlibbioc_1.22.0    plyr_1.8.4    AnnotationHub_2.8.1
[66] grid_3.4.2    crayon_1.3.4    lattice_0.20-35    splines_3.4.2    annotate_1.54.0
[71] locfit_1.5-9.1     knitr_1.20    pillar_1.3.0    geneplotter_1.54.0    biomaRt_2.30.0
[76] XML_3.98-1.16    glue_1.3.0    biovizBase_1.24.0     latticeExtra_0.6-28    data.table_1.11.8
[81] deSolve_1.14    httpuv_1.3.3    gtable_0.2.0    purrr_0.2.5    assertthat_0.2.0
[86] ggplot2_3.1.0    mime_0.6    xtable_1.8-3    AnnotationFilter_1.0.0    survival_2.41-3
[91] tibble_1.4.2    GenomicAlignments_1.12.2      memoise_1.0.0    bindrcpp_0.2.2     cluster_2.0.6
[96] statmod_1.4.30     interactiveDisplayBase_1.12.0

ADD COMMENTlink modified 9 months ago • written 10 months ago by abdul rawoof60
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