Closed borexino closed 1 year ago
Hi @borexino
I think your error comes from a typo in the code:
label.meta <- - create.label(meta=meta,
label="Sex", case="female")
This line has a -
too much :)
It should be:
label.meta <- create.label(meta=meta,
label="Sex", case="female")
The function seems to work well since the message said that the function was finished :D
However, since you are starting from a phyloseq
, you can just create a SIAMCAT
object from it directly:
sc.obj <- siamcat(phyloseq= pseq_genus, label='Sex', case='female')
This should work better :)
Cheers Jakob
No incredible! I was going crazy for this! Sorry and Thx!
My code is here:
Error got:
Dataframes structure/summary:
R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale: [1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] microbiome_1.14.0 ggplot2_3.3.5 SIAMCAT_1.99.3 mlr3_0.13.3 phyloseq_1.36.0
loaded via a namespace (and not attached): [1] nlme_3.1-157 matrixStats_0.61.0 bitops_1.0-7 progress_1.2.2 RColorBrewer_1.1-2
[6] bbotk_0.5.2 PRROC_1.3.1 GenomeInfoDb_1.28.4 numDeriv_2016.8-1.1 mlr3learners_0.5.2
[11] tools_4.1.0 backports_1.4.1 utf8_1.2.2 R6_2.5.1 vegan_2.5-7
[16] DBI_1.1.2 BiocGenerics_0.38.0 mgcv_1.8-39 colorspace_2.0-3 permute_0.9-7
[21] rhdf5filters_1.4.0 ade4_1.7-18 withr_2.5.0 mlr3misc_0.10.0 prettyunits_1.1.1
[26] tidyselect_1.1.2 gridExtra_2.3 compiler_4.1.0 glmnet_4.1-3 cli_3.2.0
[31] Biobase_2.52.0 lgr_0.4.3 scales_1.1.1 checkmate_2.0.0 palmerpenguins_0.1.0
[36] mlr3tuning_0.12.1 stringr_1.4.0 digest_0.6.29 minqa_1.2.4 paradox_0.8.0
[41] XVector_0.32.0 pkgconfig_2.0.3 parallelly_1.30.0 lme4_1.1-28 rlang_1.0.2
[46] rstudioapi_0.13 shape_1.4.6 generics_0.1.2 jsonlite_1.8.0 dplyr_1.0.8
[51] RCurl_1.98-1.6 magrittr_2.0.2 GenomeInfoDbData_1.2.6 biomformat_1.20.0 Matrix_1.4-1
[56] Rcpp_1.0.8.3 munsell_0.5.0 S4Vectors_0.30.2 Rhdf5lib_1.14.2 fansi_1.0.3
[61] ape_5.6-2 lifecycle_1.0.1 infotheo_1.2.0 pROC_1.18.0 stringi_1.7.6
[66] MASS_7.3-56 zlibbioc_1.38.0 Rtsne_0.15 rhdf5_2.36.0 plyr_1.8.7
[71] grid_4.1.0 LiblineaR_2.10-12 parallel_4.1.0 listenv_0.8.0 crayon_1.5.1
[76] lattice_0.20-45 Biostrings_2.60.2 splines_4.1.0 multtest_2.48.0 hms_1.1.1
[81] beanplot_1.2 pillar_1.7.0 igraph_1.2.11 uuid_1.0-4 boot_1.3-28
[86] reshape2_1.4.4 codetools_0.2-18 stats4_4.1.0 glue_1.6.2 data.table_1.14.2
[91] nloptr_2.0.0 vctrs_0.3.8 foreach_1.5.2 tidyr_1.2.0 gtable_0.3.0
[96] purrr_0.3.4 future_1.24.0 assertthat_0.2.1 gridBase_0.4-7 survival_3.3-1
[101] tibble_3.1.6 lmerTest_3.1-3 iterators_1.0.14 IRanges_2.26.0 cluster_2.1.2
[106] corrplot_0.92 globals_0.14.0 ellipsis_0.3.2