DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
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Dakarai ▴ 10
Last seen 12 months ago
United States

I am trying to perform differential exon usage analysis using DEXSeq. I cannot create a DEXSeqDataset object using count files generated from and gff file generated from I found other questions where the suggestion was to check if there was a discrepancy betweem the number of lines in count files and lines corresponding to 'exonic_part' in the gff file. I've checked this and found that all counts files match and correspond with the gff file. Can anyone offer a suggestion to fix this?

My code returns: Error in FUN(X[[i]], ...) : subscript out of bounds

#Output of list.files() in working directory
 "3-31-22input_juncs_DI_pA_all_exons.filtered.gff"                                                                                                                  "KO_1_8.counts.txt"   "KO_3_1.counts.txt" "KO_3_2.counts.txt"                                                                                                      "KO_3_3.counts.txt" "WT_3_6.counts.txt"                                                                                                                                              "WT_3_7.counts.txt"   "WT_3_8.counts.txt"   

countFiles <- list.files(pattern = '.counts', full.names=TRUE)
flattenedFile <- list.files(pattern-'.gff',full.names=TRUE)

sampleTable <- data.frame(row.names=c('KO_1_8','KO_3_1','KO_3_2','KO_3_3','WT_1_7','WT_3_6','WT_3_7','WT_3_8'), condition = c('KO','KO','KO','KO','WT','WT','WT','WT'),libType = c('paired-end','paired-end','paired-end','paired-end','paired-end','paired-end','paired-end','paired-end'))

dxd <- DEXSeqDataSetFromHTSeq(countFiles, 
sampleData=sampleTable, design= ~sample+exon+condition:exon, flattenedfile=flattenedFile) #problematic line

#output of sessionInfo( ):

R version 4.1.3 (2022-03-10)                                                                                                                                            Platform: x86_64-pc-linux-gnu (64-bit)                                                                                                                                  Running under: Ubuntu 20.04.3 LTS                                                                                                                                                                                                                                                                                                               Matrix products: default                                                                                                                                                BLAS:   /usr/lib/x86_64-linux-gnu/blas/                                                                                                                 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/                                                                                                                                                                                                                                                                                     locale:                                                                                                                                                                  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8                                                                                                       [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8                                                                                                   [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C                                                                                                         [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C                                                                                                                                                                                                                                                                          attached base packages:                                                                                                                                                 [1] stats4    stats     graphics  grDevices utils     datasets  methods                                                                                                 [8] base                                                                                                                                                                                                                                                                                                                                        other attached packages:                                                                                                                                                 [1] DEXSeq_1.40.0               RColorBrewer_1.1-3                                                                                                                      [3] AnnotationDbi_1.56.2        DESeq2_1.34.0                                                                                                                           [5] SummarizedExperiment_1.24.0 GenomicRanges_1.46.1                                                                                                                    [7] GenomeInfoDb_1.30.1         IRanges_2.28.0                                                                                                                          [9] S4Vectors_0.32.4            MatrixGenerics_1.6.0                                                                                                                   [11] matrixStats_0.61.0          Biobase_2.54.0                                                                                                                         [13] BiocGenerics_0.40.0         BiocParallel_1.28.3                                                                                                                                                                                                                                                                                            loaded via a namespace (and not attached):                                                                                                                               [1] httr_1.4.2             bit64_4.0.5            splines_4.1.3                                                                                                         [4] assertthat_0.2.1       statmod_1.4.36         BiocFileCache_2.2.1                                                                                                   [7] blob_1.2.2             Rsamtools_2.10.0       GenomeInfoDbData_1.2.7                                                                                               [10] progress_1.2.2         pillar_1.7.0           RSQLite_2.2.12                                                                                                       [13] lattice_0.20-45        glue_1.6.2             digest_0.6.29                                                                                                        [16] XVector_0.34.0         colorspace_2.0-3       Matrix_1.4-1                                                                                                         [19] XML_3.99-0.9           pkgconfig_2.0.3        biomaRt_2.50.3                                                                                                       [22] genefilter_1.76.0      zlibbioc_1.40.0        purrr_0.3.4                                                                                                          [25] xtable_1.8-4           scales_1.1.1           tibble_3.1.6                                                                                                         [28] annotate_1.72.0        KEGGREST_1.34.0        generics_0.1.2                                                                                                       [31] ggplot2_3.3.5          ellipsis_0.3.2         cachem_1.0.6                                                                                                         [34] cli_3.2.0              survival_3.3-1         magrittr_2.0.3                                                                                                       [37] crayon_1.5.1           memoise_2.0.1          fansi_1.0.3                                                                                                          [40] xml2_1.3.3             hwriter_1.3.2          tools_4.1.3                                                                                                          [43] prettyunits_1.1.1      hms_1.1.1              lifecycle_1.0.1                                                                                                      [46] stringr_1.4.0          munsell_0.5.0          locfit_1.5-9.5                                                                                                       [49] DelayedArray_0.20.0    Biostrings_2.62.0      compiler_4.1.3                                                                                                       [52] rlang_1.0.2            grid_4.1.3             RCurl_1.98-1.6                                                                                                       [55] rappdirs_0.3.3         bitops_1.0-7           gtable_0.3.0                                                                                                         [58] curl_4.3.2             DBI_1.1.2              R6_2.5.1                                                                                                             [61] dplyr_1.0.8            fastmap_1.1.0          bit_4.0.4                                                                                                            [64] utf8_1.2.2             filelock_1.0.2         stringi_1.7.6                                                                                                        [67] parallel_4.1.3         Rcpp_1.0.8.3           vctrs_0.4.0                                                                                                          [70] geneplotter_1.72.0     png_0.1-7              dbplyr_2.1.1                                                                                                         [73] tidyselect_1.1.2
R DEXSeq SequenceAnnotation RNASeqData • 516 views
Entering edit mode

Hello! I had the same issue it was answered. Its the quotes made by newer versions of HTSeq. See Arthur's answer here: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq) Good luck!!

Entering edit mode

Thank you so much! Sorry for the late response, was pulled away by some other work.


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