Entering edit mode
Hi Kristoffer Vitting-Seerup,
I am trying to use IsoformSwitchAnalyzeR to analyze my RNAseq data. When I trying to run analyzeAlternativeSplicing, I got error:
Error in `[.data.frame`(localExonSkippingIndex, 1) : undefined columns selected
Is there any thing I missed?
Here is my code:
library(IsoformSwitchAnalyzeR) aSwitchList <- importRdata( isoformCountMatrix = counts, isoformRepExpression = exp, designMatrix = data.frame(sampleID=colnames(counts)[-1], condition=sub("_rep.", "", colnames(counts)[-1])), isoformExonAnnoation = localAnnotation) aSwitchList <- preFilter(aSwitchList, geneExpressionCutoff = 1, isoformExpressionCutoff = 0, removeSingleIsoformGenes = TRUE) aSwitchList <- isoformSwitchTestDRIMSeq( aSwitchList ) library(BSgenome.Drerio.UCSC.danRer10) exampleSwitchListAnalyzed <- analyzeORF( aSwitchList, genomeObject= Drerio) exampleSwitchListAnalyzed <- analyzeAlternativeSplicing( exampleSwitchListAnalyzed )
Here is the data:
counts table: isoform_id inj_rep1 inj_rep2 uni_rep1 uni_rep2 ENSDART00000097631.4 ENSDART00000097631 49.91803 52.16553 76.69467 78.242030 ENSDART00000169443.1 ENSDART00000169443 187.08195 223.83441 196.30529 151.757982 ENSDART00000170158.1 ENSDART00000170158 394.17787 397.74052 0.00000 5.638381 ENSDART00000171794.2 ENSDART00000171794 372.23452 477.79328 275.56682 260.489120 ENSDART00000164713.1 ENSDART00000164713 448.81833 432.34869 2118.43899 2272.995210 ENSDART00000168732.1 ENSDART00000168732 1332.93794 1253.32564 6279.55023 5764.982906 ENSDART00000167905.1 ENSDART00000167905 1332.93794 1253.32564 3329.92554 4071.962573 ENSDART00000170411.1 ENSDART00000170411 179.87738 196.09420 139.91539 137.285373 ENSDART00000169846.1 ENSDART00000169846 471.68002 418.38313 104.52679 77.551425 ENSDART00000169539.1 ENSDART00000169539 228.64206 303.15667 116.05971 116.691904 ENSDART00000168709.1 ENSDART00000168709 170.52131 215.26682 39.42153 35.757866 ENSDART00000167456.1 ENSDART00000167456 71.67936 37.00505 44.85629 21.031085 ENSDART00000158062.1 ENSDART00000158062 408.11734 451.99495 74.14371 66.968916 ENSDART00000172394.1 ENSDART00000172394 626.78916 471.64739 213.52186 264.217355 ENSDART00000170637.1 ENSDART00000170637 290.06519 427.62319 492.98162 502.917689 ENSDART00000176601.1 ENSDART00000176601 147.67898 130.11751 142.12726 129.322780 ENSDART00000127085.2 ENSDART00000127085 130.32099 141.88252 66.87272 80.677221 ENSDART00000169268.1 ENSDART00000169268 155.24162 129.12446 103.22608 59.437924 ENSDART00000167000.1 ENSDART00000167000 256.67582 284.13010 327.04572 367.689609 ENSDART00000166248.1 ENSDART00000166248 728.42970 652.77464 626.33181 629.949785 ENSDART00000163725.1 ENSDART00000163725 145.35091 162.39590 205.89374 237.519453 ENSDART00000108528.3 ENSDART00000108528 302.88237 249.19433 0.00000 0.000000 ENSDART00000042086.5 ENSDART00000042086 1570.76676 1454.40982 1709.10632 1775.480527 expression table: isoform_id inj_rep1 inj_rep2 uni_rep1 uni_rep2 ENSDART00000097631.4 ENSDART00000097631 0.8402959 0.8180524 1.6638950 2.0734843 ENSDART00000169443.1 ENSDART00000169443 2.4496215 2.7303391 3.3127219 3.1282718 ENSDART00000170158.1 ENSDART00000170158 13.8070987 12.9787441 0.0000000 0.3109213 ENSDART00000171794.2 ENSDART00000171794 4.1447246 4.9561189 3.9545024 4.5661950 ENSDART00000164713.1 ENSDART00000164713 3.6164655 3.2454172 21.9996404 28.8335483 ENSDART00000168732.1 ENSDART00000168732 7.7022575 6.7467509 46.7651711 52.4435354 ENSDART00000167905.1 ENSDART00000167905 7.7022575 6.7467509 24.7986770 37.0422804 ENSDART00000170411.1 ENSDART00000170411 1.0410377 1.0572490 1.0436173 1.2508349 ENSDART00000169846.1 ENSDART00000169846 2.7255590 2.2521894 0.7784337 0.7054784 ENSDART00000169539.1 ENSDART00000169539 1.3796176 1.7040895 0.9025473 1.1084834 ENSDART00000168709.1 ENSDART00000168709 1.4195597 1.6694551 0.4229552 0.4686325 ENSDART00000167456.1 ENSDART00000167456 1.7901539 0.8609540 1.4437951 0.8268825 ENSDART00000158062.1 ENSDART00000158062 10.0899049 10.4101805 2.3624478 2.6065204 ENSDART00000172394.1 ENSDART00000172394 5.7010487 3.9964405 2.5030037 3.7833842 ENSDART00000170637.1 ENSDART00000170637 2.6383286 3.6234074 5.7789626 7.2013848 ENSDART00000176601.1 ENSDART00000176601 2.1112942 1.7329597 2.6187457 2.9106563 ENSDART00000127085.2 ENSDART00000127085 1.6775814 1.7014562 1.1094408 1.6349558 ENSDART00000169268.1 ENSDART00000169268 8.4098364 6.5164423 7.2070031 5.0690765 ENSDART00000167000.1 ENSDART00000167000 2.8536987 2.9428156 4.6861644 6.4356194 ENSDART00000166248.1 ENSDART00000166248 7.6195214 6.3610084 8.4436534 10.3736553 ENSDART00000163725.1 ENSDART00000163725 0.9165777 0.9540019 1.6733260 2.3579606 ENSDART00000108528.3 ENSDART00000108528 2.0157871 1.5450106 0.0000000 0.0000000 ENSDART00000042086.5 ENSDART00000042086 11.2282419 9.6852203 15.7454480 19.9802908 localAnnotation were downloaded from ftp://ftp.ensembl.org/pub/release-91/gtf/danio_rerio/ and then subset by the isoform_id
Sessioninfo:
R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.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 stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BSgenome.Drerio.UCSC.danRer10_1.4.2 BSgenome_1.48.0 Biostrings_2.48.0 XVector_0.20.0 IsoformSwitchAnalyzeR_1.2.0 [6] cummeRbund_2.22.0 Gviz_1.24.0 rtracklayer_1.40.6 GenomicRanges_1.32.7 GenomeInfoDb_1.16.0 [11] IRanges_2.14.12 S4Vectors_0.18.3 fastcluster_1.1.25 reshape2_1.4.3 ggplot2_3.0.0 [16] RSQLite_2.1.1 BiocGenerics_0.26.0 loaded via a namespace (and not attached): [1] ProtGenerics_1.12.0 bitops_1.0-6 matrixStats_0.54.0 bit64_0.9-7 RColorBrewer_1.1-2 progress_1.2.0 [7] httr_1.3.1 tools_3.5.1 backports_1.1.2 R6_2.2.2 rpart_4.1-13 Hmisc_4.1-1 [13] DBI_1.0.0 lazyeval_0.2.1 colorspace_1.3-2 nnet_7.3-12 withr_2.1.2 tidyselect_0.2.4 [19] gridExtra_2.3 prettyunits_1.0.2 VennDiagram_1.6.20 curl_3.2 bit_1.1-14 compiler_3.5.1 [25] Biobase_2.40.0 formatR_1.5 htmlTable_1.12 DelayedArray_0.6.6 scales_1.0.0 checkmate_1.8.5 [31] readr_1.1.1 stringr_1.3.1 digest_0.6.17 Rsamtools_1.32.3 foreign_0.8-71 base64enc_0.1-3 [37] dichromat_2.0-0 pkgconfig_2.0.2 htmltools_0.3.6 limma_3.36.5 ensembldb_2.4.1 htmlwidgets_1.3 [43] rlang_0.2.2 rstudioapi_0.7 bindr_0.1.1 jsonlite_1.5 BiocParallel_1.14.2 acepack_1.4.1 [49] dplyr_0.7.6 VariantAnnotation_1.26.1 RCurl_1.95-4.11 magrittr_1.5 GenomeInfoDbData_1.1.0 Formula_1.2-3 [55] futile.logger_1.4.3 Matrix_1.2-14 Rcpp_0.12.19 munsell_0.5.0 edgeR_3.22.4 stringi_1.2.4 [61] MASS_7.3-50 SummarizedExperiment_1.10.1 zlibbioc_1.26.0 plyr_1.8.4 blob_1.1.1 crayon_1.3.4 [67] lattice_0.20-35 DRIMSeq_1.8.0 splines_3.5.1 GenomicFeatures_1.32.2 hms_0.4.2 locfit_1.5-9.1 [73] knitr_1.20 pillar_1.3.0 biomaRt_2.36.1 futile.options_1.0.1 XML_3.98-1.16 glue_1.3.0 [79] biovizBase_1.28.2 latticeExtra_0.6-28 lambda.r_1.2.3 data.table_1.11.4 gtable_0.2.0 purrr_0.2.5 [85] assertthat_0.2.0 AnnotationFilter_1.4.0 survival_2.42-6 tibble_1.4.2 GenomicAlignments_1.16.0 AnnotationDbi_1.42.1 [91] memoise_1.1.0 tximport_1.8.0 bindrcpp_0.2.2 cluster_2.0.7-1