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Hi , I am trying to create a metagene plot using R. i mapped using star and files were indexed. But when i try to plot i'm getting error which i'm not sure. Can you please help me with this.
> bam_files <-c(system.file("extdata/ Aligned.sortedByCoord.out.bam", package="metagene"))
> regions <- c(system.file("extdata/list2.bed", package="metagene"))
> mg <- metagene$new(regions = regions, bam_files = bam_files, assay = 'rnaseq', paired_end = TRUE)
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error: scan() expected 'an integer', got '3337105133371051'
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] metagene_2.24.0 BiocParallel_1.28.3 R6_2.5.1
[4] GenomicAlignments_1.30.0 Rsamtools_2.10.0 pasillaBamSubset_0.30.0
[7] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 BSgenome_1.60.0 rtracklayer_1.54.0
[10] Biostrings_2.62.0 XVector_0.34.0 GenomicFeatures_1.46.3
[13] AnnotationDbi_1.56.2 gread_0.99.2 SummarizedExperiment_1.24.0
[16] Biobase_2.54.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0
[19] IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0
[22] MatrixGenerics_1.6.0 matrixStats_0.61.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.24.0 bitops_1.0-7 bit64_4.0.5 filelock_1.0.2 progress_1.2.2
[6] httr_1.4.2 tools_4.1.2 utf8_1.2.2 KernSmooth_2.23-20 DBI_1.1.2
[11] lazyeval_0.2.2 colorspace_2.0-2 withr_2.4.3 tidyselect_1.1.1 prettyunits_1.1.1
[16] bit_4.0.4 curl_4.3.2 compiler_4.1.2 EnsDb.Hsapiens.v86_2.99.0 xml2_1.3.3
[21] DelayedArray_0.20.0 caTools_1.18.2 scales_1.1.1 rappdirs_0.3.3 stringr_1.4.0
[26] digest_0.6.29 pkgconfig_2.0.3 dbplyr_2.1.1 fastmap_1.1.0 ensembldb_2.16.4
[31] rlang_0.4.12 rstudioapi_0.13 RSQLite_2.2.9 BiocIO_1.4.0 generics_0.1.1
[36] gtools_3.9.2 dplyr_1.0.7 RCurl_1.98-1.5 magrittr_2.0.1 GenomeInfoDbData_1.2.7
[41] muStat_1.7.0 Matrix_1.4-0 Rcpp_1.0.8 munsell_0.5.0 fansi_1.0.2
[46] lifecycle_1.0.1 stringi_1.7.6 yaml_2.2.1 zlibbioc_1.40.0 gplots_3.1.1
[51] BiocFileCache_2.2.0 grid_4.1.2 blob_1.2.2 parallel_4.1.2 crayon_1.4.2
[56] lattice_0.20-45 hms_1.1.1 KEGGREST_1.34.0 pillar_1.6.4 rjson_0.2.21
[61] biomaRt_2.50.2 XML_3.99-0.8 glue_1.6.0 data.table_1.14.2 BiocManager_1.30.16
[66] png_0.1-7 vctrs_0.3.8 gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1
[71] cachem_1.0.6 ggplot2_3.3.5 restfulr_0.0.13 AnnotationFilter_1.16.0 snow_0.4-4
[76] tibble_3.1.6 memoise_2.0.1 ellipsis_0.3.2
I came across the same problem, have you solved it?