Error in xj[i] : invalid subscript type 'list' when running jDUreport on Aspli
0
0
Entering edit mode
Randall • 0
@d3ca9733
Last seen 10 days ago
United States

Hi all, I got this error using the Aspli package. I cannot seem to fix it. Worked before. All packages updated and still fails. Thanks!

#RNA-seq BAM files
flsall <- dir(getwd(),".bam")
flsall<-paste0(getwd(),'/',flsall)
names(flsall)<-gsub('.bam','',dir(getwd(),".bam"))
BAMFiles <- flsall
#RNA-seq GTF file
flsgtf <- dir(getwd(),".gtf")
genomeTxDb <- makeTxDbFromGFF(file = flsgtf)
features <- binGenome(genomeTxDb)
#Combine BAM and target files
targets <- data.frame(row.names = paste0('Sample',c(1:9)),
bam = BAMFiles[1:9],
f1 = c( 'treatment','control','treatment','treatment','treatment','treatment','control','control','control'),
stringsAsFactors = FALSE)
mBAMs <- data.frame( bam = sub("_[012]","",targets$bam[c(1,4)]),
condition = c("control","treatment"))
#Read counting
gbcounts <- gbCounts(features=features, targets=targets,
minReadLength = 295, maxISize = 50000, libType="PE")
#Junction-based de-novo counting
asd <- jCounts(counts=gbcounts, features=features, minReadLength=295, libType="PE")
#Differential gene expression
gb <- gbDUreport(gbcounts, contrast = c(-1,1))
#Differential junction usage
jdur <- jDUreport(asd, contrast=c(-1,1), strongFilter=TRUE, useSubset = FALSE)

library(ASpli)
library(GenomicFeatures)
#Differential junction usage
jdur <- jDUreport(asd, contrast=c(-1,1), strongFilter=TRUE, useSubset = FALSE)
Running junctionsPJU test
Running junctionsPIR test
Error in xj[i] : invalid subscript type 'list'
sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] BiocManager_1.30.22 GenomicFeatures_1.54.4 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 ASpli_2.12.0
[6] AnnotationDbi_1.64.1 IRanges_2.36.0 S4Vectors_0.40.2 Biobase_2.60.0 BiocGenerics_0.48.1
[11] edgeR_4.0.16 limma_3.58.1

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0 magrittr_2.0.3 rmarkdown_2.26
[5] BiocIO_1.12.0 zlibbioc_1.48.2 vctrs_0.6.5 memoise_2.0.1
[9] Rsamtools_2.18.0 RCurl_1.98-1.14 base64enc_0.1-3 htmltools_0.5.8
[13] S4Arrays_1.2.1 progress_1.2.3 curl_5.2.1 SparseArray_1.2.4
[17] Formula_1.2-5 htmlwidgets_1.6.4 plyr_1.8.9 Gviz_1.46.1
[21] cachem_1.0.8 GenomicAlignments_1.38.2 igraph_2.0.3 lifecycle_1.0.4
[25] pkgconfig_2.0.3 Matrix_1.6-5 R6_2.5.1 fastmap_1.1.1
[29] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0 digest_0.6.35 colorspace_2.1-0
[33] Hmisc_5.1-2 RSQLite_2.3.5 filelock_1.0.3 fansi_1.0.6
[37] httr_1.4.7 abind_1.4-5 compiler_4.3.3 bit64_4.0.5
[41] htmlTable_2.4.2 backports_1.4.1 BiocParallel_1.34.2 DBI_1.2.2
[45] UpSetR_1.4.0 biomaRt_2.58.2 MASS_7.3-60.0.1 rappdirs_0.3.3
[49] DelayedArray_0.28.0 rjson_0.2.21 tools_4.3.3 foreign_0.8-86
[53] nnet_7.3-19 glue_1.7.0 restfulr_0.0.15 grid_4.3.3
[57] checkmate_2.3.1 cluster_2.1.6 generics_0.1.3 gtable_0.3.5
[61] BSgenome_1.70.2 tidyr_1.3.1 ensembldb_2.26.0 data.table_1.15.2
[65] hms_1.1.3 xml2_1.3.6 utf8_1.2.4 XVector_0.42.0
[69] pillar_1.9.0 stringr_1.5.1 splines_4.3.3 dplyr_1.1.4
[73] BiocFileCache_2.10.2 lattice_0.22-6 deldir_2.0-4 rtracklayer_1.62.0
[77] bit_4.0.5 biovizBase_1.50.0 tidyselect_1.2.1 locfit_1.5-9.9
[81] Biostrings_2.70.3 knitr_1.46 gridExtra_2.3 ProtGenerics_1.34.0
[85] SummarizedExperiment_1.32.0 xfun_0.43 statmod_1.5.0 matrixStats_1.2.0
[89] DT_0.33 stringi_1.8.3 lazyeval_0.2.2 yaml_2.3.8
[93] evaluate_0.23 codetools_0.2-19 interp_1.1-6 tibble_3.2.1
[97] cli_3.6.2 rpart_4.1.23 pbmcapply_1.5.1 munsell_0.5.1
[101] dichromat_2.0-0.1 Rcpp_1.0.12 dbplyr_2.5.0 png_0.1-8
[105] XML_3.99-0.16.1 ggplot2_3.5.1 blob_1.2.4 prettyunits_1.2.0
[109] jpeg_0.1-10 latticeExtra_0.6-30 AnnotationFilter_1.26.0 bitops_1.0-7
[113] VariantAnnotation_1.48.1 scales_1.3.0 purrr_1.0.2 crayon_1.5.2
[117] BiocStyle_2.30.0 rlang_1.1.3 KEGGREST_1.42.0

traceback()
6: [.data.frame(J3, reliables, )
5: J3[reliables, ]
4: .makeJunctions(data, targets, start_J1, start_J2, start_J3, minAvgCounts,
filterWithContrasted, contrast, strongFilter)
3: .junctionDUreportExt(asd, minAvgCounts, contrast, filterWithContrasted,
runUniformityTest, mergedBams, maxPValForUniformityCheck,
strongFilter, maxConditionsForDispersionEstimate, formula,
coef, maxFDRForParticipation, useSubset)
2: jDUreport(asd, contrast = c(-1, 1), strongFilter = TRUE, useSubset = FALSE)
1: jDUreport(asd, contrast = c(-1, 1), strongFilter = TRUE, useSubset = FALSE)
ASpli • 88 views
ADD COMMENT

Login before adding your answer.

Traffic: 375 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6