Entering edit mode
If I run testForDEU()
, the resulting DEXSeqDataSet
object only contains TRUE
or NA
and no FALSE
entries for mcols(dxd)$fullBetaConv
. According to the summary stats, it seems that NA
can be interpreted as FALSE
. Is this a bug?
> sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] RSQLite_2.2.14 stageR_1.18.0 rtracklayer_1.56.1 dplyr_1.0.9 ArvadosR_2.4.0
[6] DEXSeq_1.42.0 RColorBrewer_1.1-3 AnnotationDbi_1.58.0 DESeq2_1.36.0 SummarizedExperiment_1.26.1
[11] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0 MatrixGenerics_1.8.1
[16] matrixStats_0.62.0 Biobase_2.56.0 BiocGenerics_0.42.0 BiocParallel_1.30.3
loaded via a namespace (and not attached):
[1] bitops_1.0-7 bit64_4.0.5 filelock_1.0.2 progress_1.2.2 httr_1.4.3 tools_4.2.0
[7] utf8_1.2.2 R6_2.5.1 DBI_1.1.2 colorspace_2.0-3 tidyselect_1.1.2 prettyunits_1.1.1
[13] bit_4.0.4 curl_4.3.2 compiler_4.2.0 cli_3.3.0 xml2_1.3.3 DelayedArray_0.22.0
[19] scales_1.2.0 genefilter_1.78.0 rappdirs_0.3.3 stringr_1.4.0 digest_0.6.29 Rsamtools_2.12.0
[25] XVector_0.36.0 pkgconfig_2.0.3 dbplyr_2.2.0 fastmap_1.1.0 rlang_1.0.2 rstudioapi_0.13
[31] BiocIO_1.6.0 generics_0.1.2 hwriter_1.3.2.1 RCurl_1.98-1.7 magrittr_2.0.3 GenomeInfoDbData_1.2.8
[37] Matrix_1.4-1 Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.3 lifecycle_1.0.1 stringi_1.7.6
[43] yaml_2.3.5 zlibbioc_1.42.0 BiocFileCache_2.4.0 grid_4.2.0 blob_1.2.3 parallel_4.2.0
[49] crayon_1.5.1 lattice_0.20-45 Biostrings_2.64.0 splines_4.2.0 annotate_1.74.0 hms_1.1.1
[55] KEGGREST_1.36.3 locfit_1.5-9.5 pillar_1.7.0 rjson_0.2.21 geneplotter_1.74.0 codetools_0.2-18
[61] biomaRt_2.52.0 XML_3.99-0.10 glue_1.6.2 png_0.1-7 vctrs_0.4.1 gtable_0.3.0
[67] purrr_0.3.4 assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.6 xtable_1.8-4 restfulr_0.0.15
[73] survival_3.3-1 tibble_3.1.7 GenomicAlignments_1.32.0 memoise_2.0.1 statmod_1.4.36 ellipsis_0.3.2