I recently updated some packages, which I think is interfering with the resultsNames() function. I've tried to test it on premade datasets to make sure that it's not a personal data issue, and am running into the same problem.

The below function uses a phyloseq dataset, which is similar to my dataset and showing the same issue.

> library(phyloseq)
> data(soilrep)
> prevalence_subset = soilrep

> map = data.frame(sample_data(prevalence_subset))

> OTU_data = data.frame(otu_table(prevalence_subset))
> OTU_data = OTU_data + 1
> OTU_data = otu_table(OTU_data, taxa_are_rows = TRUE)
> otu_table(prevalence_subset) = OTU_data

> diagdds_1 = phyloseq_to_deseq2(prevalence_subset, ~Treatment)
converting counts to integer mode
> diagdds_1 = DESeq(diagdds_1, test="Wald", fitType="local", quiet = TRUE)
> current_RN = resultsNames(diagdds_1)

> current_RN 
[1] "Intercept"  "Treatment1" "Treatment2" "Treatment3"
> #I'd expect it to be call on the variable names; "UC" "UU" "WU" "WC"

I've also tried running the script available on the Bioconductor subpage, to make sure it wasn't a phyloseq issue. Everything ran without error until I reached line 151, where I ran into the same problem.

> ## ----lfcShrink----------------------------------------------------------------
> resultsNames(dds)
[1] "Intercept"  "condition1"
> resLFC <- lfcShrink(dds, coef="condition_treated_vs_untreated", type="apeglm")
Error in lfcShrink(dds, coef = "condition_treated_vs_untreated", type = "apeglm") : 
  coef %in% resultsNamesDDS is not TRUE

Here are the current package versions I'm using.

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] datasets  parallel  stats4    stats     graphics  grDevices utils     methods   base     

other attached packages:
 [1] phyloseq_1.30.0             airway_1.6.0                tximeta_1.4.5               tximportData_1.14.0        
 [5] readr_1.3.1                 tximport_1.14.2             DESeq2_1.26.0               vegan_2.5-6                
 [9] lattice_0.20-41             permute_0.9-5               pime_0.1.0                  stringr_1.4.0              
[13] ggplot2_3.3.2               SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.1        
[17] matrixStats_0.56.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[21] IRanges_2.20.2              S4Vectors_0.24.4            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
  [1] backports_1.1.8          Hmisc_4.4-0              BiocFileCache_1.10.2     plyr_1.8.6               igraph_1.2.5            
  [6] lazyeval_0.2.2           splines_3.6.2            digest_0.6.25            foreach_1.5.0            ensembldb_2.10.2        
 [11] htmltools_0.5.0          magrittr_1.5             checkmate_2.0.0          memoise_1.1.0            cluster_2.1.0           
 [16] doParallel_1.0.15        Biostrings_2.54.0        annotate_1.64.0          askpass_1.1              prettyunits_1.1.1       
 [21] jpeg_0.1-8.1             colorspace_1.4-1         blob_1.2.1               rappdirs_0.3.1           xfun_0.15               
 [26] dplyr_1.0.0              crayon_1.3.4             RCurl_1.98-1.2           jsonlite_1.7.0           genefilter_1.68.0       
 [31] survival_3.2-3           iterators_1.0.12         ape_5.4                  glue_1.4.1               gtable_0.3.0            
 [36] zlibbioc_1.32.0          XVector_0.26.0           Rhdf5lib_1.8.0           scales_1.1.1             DBI_1.1.0               
 [41] Rcpp_1.0.5               xtable_1.8-4             progress_1.2.2           htmlTable_2.0.1          foreign_0.8-72          
 [46] bit_1.1-15.2             Formula_1.2-3            htmlwidgets_1.5.1        httr_1.4.1               RColorBrewer_1.1-2      
 [51] acepack_1.4.1            ellipsis_0.3.1           pkgconfig_2.0.3          XML_3.99-0.3             farver_2.0.3            
 [56] nnet_7.3-14              dbplyr_1.4.4             locfit_1.5-9.4           tidyselect_1.1.0         labeling_0.3            
 [61] rlang_0.4.6              reshape2_1.4.4           AnnotationDbi_1.48.0     munsell_0.5.0            tools_3.6.2             
 [66] generics_0.0.2           RSQLite_2.2.0            ade4_1.7-15              ranger_0.12.1            biomformat_1.14.0       
 [71] knitr_1.29               bit64_0.9-7              purrr_0.3.4              randomForest_4.6-14      AnnotationFilter_1.10.0 
 [76] nlme_3.1-148             biomaRt_2.42.1           compiler_3.6.2           rstudioapi_0.11          curl_4.3                
 [81] png_0.1-7                tibble_3.0.2             geneplotter_1.64.0       stringi_1.4.6            GenomicFeatures_1.38.2  
 [86] forcats_0.5.0            ProtGenerics_1.18.0      Matrix_1.2-18            microbiome_1.8.0         multtest_2.42.0         
 [91] vctrs_0.3.1              pillar_1.4.4             lifecycle_0.2.0          BiocManager_1.30.10      data.table_1.12.8       
 [96] bitops_1.0-6             rtracklayer_1.46.0       R6_2.4.1                 latticeExtra_0.6-29      gridExtra_2.3           
[101] codetools_0.2-16         MASS_7.3-51.6            assertthat_0.2.1         rhdf5_2.30.1             openssl_1.4.2           
[106] withr_2.2.0              GenomicAlignments_1.22.1 Rsamtools_2.2.3          GenomeInfoDbData_1.2.2   mgcv_1.8-31             
[111] hms_0.5.3                grid_3.6.2               rpart_4.1-15             tidyr_1.1.0              Rtsne_0.15              
[116] base64enc_0.1-3         

Thank you so much for your time!

Here is my take on the above code snippets:

First snippet: resultsNames will be based on the colData of dds and on the design. Here the creation of the DESeqDataSet is actually being done within another function from phyloseq, so you'd have to see how they are converting your sample information (we call colData). But you can check what is being provided to DESeq2 by looking at colData(dds). This is the information DESeq() is working with and that is what determines the resultsNames.

Second snippet: when you specify coef it has to be the name of a character string in resultsNames(dds). The printed error gives you a hint to this. Since "condition_treated_vs_untreated" is not present in the vector: c("Intercept", "condition1"), it gives an error.

One issue is that I can't see any lines where DESeqDataSet is created (because they are within other functions, or not shown above), so I can't help resolve the DESeq2 side of things.