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
