Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
Entering edit mode
rubi ▴ 90
Last seen 2.9 years ago


Simple question:


How do I see what knots were selected? Anything similar to lm's

attr(terms(fit), "predvars")




> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS  10.13.6

[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  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] edge_2.4.2           Biobase_2.32.0       BiocGenerics_0.18.0  BiocInstaller_1.22.3 manhattanly_0.2.0    dplyr_0.7.4          bindrcpp_0.2        
 [8] plotly_4.7.1.9000    ggplot2_2.2.1.9000   rhdf5_2.16.0        

loaded via a namespace (and not attached):
 [1] nlme_3.1-131         bitops_1.0-6         OpenImageR_1.0.7     RColorBrewer_1.1-2   httr_1.3.1           tools_3.3.3          R6_2.2.2            
 [8] vegan_2.4-1          DBI_0.5              lazyeval_0.2.1       mgcv_1.8-17          colorspace_1.2-6     permute_0.9-4        ade4_1.7-10         
[15] withr_2.1.1          labeling_0.3         FD_1.0-12            scales_0.5.0.9000    genefilter_1.54.2    stringr_1.3.1        digest_0.6.13       
[22] tiff_0.1-5           minqa_1.2.4          jpeg_0.1-8           pkgconfig_2.0.1      htmltools_0.3.6      lme4_1.1-12          limma_3.28.21       
[29] htmlwidgets_1.2      rlang_0.2.0.9001     RSQLite_1.0.0        shiny_1.0.5          bindr_0.1            jsonlite_1.5         crosstalk_1.0.0     
[36] gtools_3.5.0         RCurl_1.95-4.8       magrittr_1.5         Matrix_1.2-12        Rcpp_0.12.14         munsell_0.4.3        S4Vectors_0.10.3    
[43] ape_4.1              abind_1.4-5          stringi_1.2.3        yaml_2.1.16          ClusterR_1.0.9       MASS_7.3-45          zlibbioc_1.18.0     
[50] plyr_1.8.4           qvalue_2.4.2         grid_3.3.3           lattice_0.20-34      splines_3.3.3        annotate_1.50.1      jackstraw_1.2       
[57] corpcor_1.6.9        reshape2_1.4.3       stats4_3.3.3         magic_1.5-8          XML_3.98-1.9         glue_1.2.0           data.table_1.10.4-3 
[64] snm_1.20.0           png_0.1-7            nloptr_1.0.4         httpuv_1.3.5         gtable_0.2.0         purrr_0.2.4          tidyr_0.8.1         
[71] assertthat_0.2.0     lfa_1.2.2            mime_0.5             xtable_1.8-2         survival_2.40-1      viridisLite_0.2.0    geometry_0.3-6      
[78] tibble_1.3.4         AnnotationDbi_1.34.4 IRanges_2.6.1        cluster_2.0.5        sva_3.20.0           gmp_0.5-13.1        
edge differential gene expression timecourse interaction • 346 views

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