I am actually already doing this (135k in matrix after reduction), however following this command:

dds <- DESeq(dds, betaPrior = TRUE, fitType = c("local"), parallel = TRUE)

It tells me Im out of application memory right at the end of DESeq, sometimes even shutting off my computer.

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DiffBind_2.4.8             ggplot2_3.0.0              DESeq2_1.16.1              SummarizedExperiment_1.6.5 DelayedArray_0.2.7        
 [6] matrixStats_0.54.0         Biobase_2.36.2             GenomicRanges_1.28.6       GenomeInfoDb_1.12.3        IRanges_2.10.5            
[11] S4Vectors_0.14.7           BiocGenerics_0.22.1        BiocParallel_1.10.1       

loaded via a namespace (and not attached):
  [1] Category_2.42.1          bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2       tools_3.4.1              backports_1.1.2         
  [7] R6_2.3.0                 rpart_4.1-13             KernSmooth_2.23-15       Hmisc_4.1-1              DBI_1.0.0                lazyeval_0.2.1          
 [13] colorspace_1.3-2         nnet_7.3-12              withr_2.1.2              tidyselect_0.2.5         gridExtra_2.3            bit_1.1-14              
 [19] compiler_3.4.1           sendmailR_1.2-1          graph_1.54.0             htmlTable_1.12           rtracklayer_1.36.6       caTools_1.17.1.1        
 [25] scales_1.0.0             checkmate_1.8.5          BatchJobs_1.7            genefilter_1.58.1        RBGL_1.52.0              stringr_1.3.1           
 [31] digest_0.6.18            Rsamtools_1.28.0         foreign_0.8-71           AnnotationForge_1.18.2   XVector_0.16.0           base64enc_0.1-3         
 [37] pkgconfig_2.0.2          htmltools_0.3.6          limma_3.32.10            htmlwidgets_1.3          rlang_0.2.2              rstudioapi_0.8          
 [43] RSQLite_2.1.1            BBmisc_1.11              GOstats_2.42.0           bindr_0.1.1              hwriter_1.3.2            gtools_3.5.0            
 [49] acepack_1.4.1            dplyr_0.7.6              RCurl_1.95-4.11          magrittr_1.5             GO.db_3.4.1              GenomeInfoDbData_0.99.0 
 [55] Formula_1.2-3            Matrix_1.2-14            Rcpp_0.12.19             munsell_0.5.0            stringi_1.2.4            yaml_2.2.0              
 [61] edgeR_3.18.1             zlibbioc_1.22.0          gplots_3.0.1             plyr_1.8.4               grid_3.4.1               blob_1.1.1              
 [67] ggrepel_0.8.0            gdata_2.18.0             crayon_1.3.4             lattice_0.20-35          Biostrings_2.44.2        splines_3.4.1           
 [73] GenomicFeatures_1.28.5   annotate_1.54.0          locfit_1.5-9.1           knitr_1.20               pillar_1.3.0             rjson_0.2.20            
 [79] systemPipeR_1.10.2       geneplotter_1.54.0       biomaRt_2.32.1           XML_3.98-1.16            glue_1.3.0               ShortRead_1.34.2        
 [85] latticeExtra_0.6-28      data.table_1.11.8        gtable_0.2.0             purrr_0.2.5              amap_0.8-16              assertthat_0.2.0        
 [91] xtable_1.8-3             survival_2.42-6          pheatmap_1.0.10          tibble_1.4.2             GenomicAlignments_1.12.2 AnnotationDbi_1.38.2    
 [97] memoise_1.1.0            bindrcpp_0.2.2           cluster_2.0.7-1          brew_1.0-6               GSEABase_1.38.2