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Nikolay Ivanov
•
0
@nikolay-ivanov-23079
Last seen 3.4 years ago
USA/New York City/Weill Cornell Medicine
I have noticed that after I run tximeta's summarizeToGene function, I get the following warning:
Warning message:
call dbDisconnect() when finished working with a connection
If I execute the same command the second time, I do not get a warning.
What does the warning mean? Will it affect my analysis?
Thank you!
library(DESeq2)
library(tximeta)
# import data
se = tximeta(coldata = dataset_metadata, type = "salmon")
# summarize transcript-level quantifications to gene-level
gse = summarizeToGene(se)
loading existing EnsDb created: 2021-02-25 02:40:59
obtaining transcript-to-gene mapping from database
loading existing gene ranges created: 2021-02-25 02:52:08
summarizing abundance
summarizing counts
summarizing length
Warning message:
call dbDisconnect() when finished working with a connection
# execute the command again
gse = summarizeToGene(se)
loading existing EnsDb created: 2021-02-25 02:40:59
obtaining transcript-to-gene mapping from database
loading existing gene ranges created: 2021-02-25 02:52:08
summarizing abundance
summarizing counts
summarizing length
# no warning message this time around
sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /pbtech_mounts/homes027/nai2008/anaconda3/envs/R_4.0/lib/libopenblasp-r0.3.10.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] tximeta_1.8.4 DESeq2_1.30.0
[3] SummarizedExperiment_1.20.0 Biobase_2.50.0
[5] MatrixGenerics_1.2.0 matrixStats_0.58.0
[7] GenomicRanges_1.42.0 GenomeInfoDb_1.26.0
[9] IRanges_2.24.0 S4Vectors_0.28.0
[11] BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.22.0 bitops_1.0-6
[3] bit64_4.0.5 RColorBrewer_1.1-2
[5] progress_1.2.2 httr_1.4.2
[7] tools_4.0.3 R6_2.5.0
[9] DBI_1.1.1 lazyeval_0.2.2
[11] colorspace_2.0-0 withr_2.4.1
[13] tidyselect_1.1.0 prettyunits_1.1.1
[15] bit_4.0.4 curl_4.3
[17] compiler_4.0.3 xml2_1.3.2
[19] DelayedArray_0.16.0 rtracklayer_1.50.0
[21] scales_1.1.1 readr_1.4.0
[23] genefilter_1.72.0 askpass_1.1
[25] rappdirs_0.3.1 stringr_1.4.0
[27] digest_0.6.27 Rsamtools_2.6.0
[29] XVector_0.30.0 pkgconfig_2.0.3
[31] htmltools_0.5.1.1 dbplyr_2.0.0
[33] fastmap_1.1.0 ensembldb_2.14.0
[35] rlang_0.4.10 rstudioapi_0.13
[37] RSQLite_2.2.3 shiny_1.6.0
[39] generics_0.1.0 jsonlite_1.7.2
[41] BiocParallel_1.24.0 dplyr_1.0.4
[43] RCurl_1.98-1.2 magrittr_2.0.1
[45] GenomeInfoDbData_1.2.4 Matrix_1.3-2
[47] Rcpp_1.0.6 munsell_0.5.0
[49] lifecycle_0.2.0 stringi_1.5.3
[51] yaml_2.2.1 zlibbioc_1.36.0
[53] BiocFileCache_1.14.0 AnnotationHub_2.22.0
[55] grid_4.0.3 blob_1.2.1
[57] promises_1.1.1 crayon_1.4.1
[59] lattice_0.20-41 Biostrings_2.58.0
[61] splines_4.0.3 GenomicFeatures_1.42.1
[63] annotate_1.68.0 hms_1.0.0
[65] locfit_1.5-9.4 pillar_1.4.7
[67] geneplotter_1.68.0 biomaRt_2.46.1
[69] XML_3.99-0.5 glue_1.4.2
[71] BiocVersion_3.12.0 BiocManager_1.30.10
[73] vctrs_0.3.6 httpuv_1.5.5
[75] gtable_0.3.0 openssl_1.4.3
[77] purrr_0.3.4 assertthat_0.2.1
[79] cachem_1.0.3 ggplot2_3.3.3
[81] mime_0.9 xtable_1.8-4
[83] AnnotationFilter_1.14.0 later_1.1.0.1
[85] survival_3.2-7 tibble_3.0.6
[87] GenomicAlignments_1.26.0 AnnotationDbi_1.52.0
[89] memoise_2.0.0 tximport_1.18.0
[91] ellipsis_0.3.1 interactiveDisplayBase_1.28.0
