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ldg21 / SGSeq

Splice event prediction and quantification from RNA-seq data
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IRanges objects don't support #3

Open OlgaVT opened 4 years ago

OlgaVT commented 4 years ago

Hi, I am trying to use SGSeq and get the error with IRanges. The commands are: >library(SGSeq) >sgfc_pred <- analyzeFeatures(si) >head(rowRanges(sgfc_pred))

SGFeatures object with 6 ranges and 0 metadata columns: Error in getListElement(x, i, ...) : IRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment

Could you, please, help me? Thank you!

>sessionInfo()

R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.3 LTS

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_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0 [2] GenomicFeatures_1.38.1
[3] AnnotationDbi_1.48.0
[4] SGSeq_1.20.0 [5] SummarizedExperiment_1.16.1
[6] DelayedArray_0.12.2
[7] BiocParallel_1.20.1 [8] matrixStats_0.55.0 [9] Biobase_2.46.0 [10] Rsamtools_2.2.1 [11] Biostrings_2.54.0 [12] XVector_0.26.0 [13] GenomicRanges_1.38.0
[14] GenomeInfoDb_1.22.0
[15] IRanges_2.20.1 [16] S4Vectors_0.24.3 [17] BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] progress_1.2.2 tidyselect_1.0.0 purrr_0.3.3 [4] lattice_0.20-38 vctrs_0.2.2 BiocFileCache_1.10.2
[7] rtracklayer_1.46.0 blob_1.2.1 XML_3.99-0.1
[10] rlang_0.4.4 pillar_1.4.2 glue_1.3.1 [13] DBI_1.1.0 rappdirs_0.3.1 bit64_0.9-7 [16] dbplyr_1.4.2 GenomeInfoDbData_1.2.2 stringr_1.4.0
[19] zlibbioc_1.32.0 memoise_1.1.0 biomaRt_2.42.0
[22] RUnit_0.4.32 curl_4.3 Rcpp_1.0.2 [25] openssl_1.4.1 bit_1.1-15.1 hms_0.5.1
[28] askpass_1.1 digest_0.6.20 stringi_1.4.3
[31] dplyr_0.8.4 grid_3.6.1 tools_3.6.1 [34] bitops_1.0-6 magrittr_1.5 RCurl_1.98-1.1 [37] RSQLite_2.2.0 tibble_2.1.3 crayon_1.3.4
[40] pkgconfig_2.0.2 Matrix_1.2-17 prettyunits_1.0.2
[43] assertthat_0.2.1 httr_1.4.1 R6_2.4.0 [46] igraph_1.2.4.2 GenomicAlignments_1.22.1 compiler_3.6.1