Issue extracting interaction information from phenopath analysis
Entering edit mode
Clara • 0
Last seen 3 days ago


I did a pseudotime analysis on a bulk RNA-seq data using phenopath. Here is the code I used to do this analysis:

x_mat <- model.matrix(~ Sex)
# sce is a SummarizedExperiment object containing expression as log2(TPM+1)
fit <- phenopath(sce, x_mat, elbo_tol = 1e-6, thin = 20) 

I get the following elbo plot. enter image description here

Now I would like to extract the information about the interaction between the latent space and my covariate (Sex). I first tried to use the interactions function, and got an error:

> interaction_results <- interactions(fit)
Error: Assigned data `sig$feature <- chi$feature <- phenopath_fit$feature_names` must be compatible with existing data.
x Existing data has 2 rows.
x Assigned data has 2000 rows.
ℹ Only vectors of size 1 are recycled.

I then tried to extract the interaction information with the 3 following functions interaction_effects, interaction_sds and significant_interactions. Running these 3 functions, I was expecting to get vectors as stated in the vignette because I only have one covariate.

Note that if P=1 (ie there is only one covariate) each of these will return a vector, while if P>1 then a matrix is returned.

Instead, I get a matrix with 2 rows for the functions interaction_effects and interaction_sds, and 2 columns for the function significant_interactions. So I don't know how to interpret these results.

Could you help me get the interaction information from my analysis?

Thank you,

Clara Benoit-Pilven

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (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/3.6/Resources/lib/libRlapack.dylib

[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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.4.0               tidyr_1.1.3                 dplyr_1.0.6                 factoextra_1.0.6            ggplot2_3.3.3               ade4_1.7-16                
 [7] phenopath_1.10.0            SummarizedExperiment_1.16.1 DelayedArray_0.12.2         BiocParallel_1.20.1         matrixStats_0.55.0          edgeR_3.28.0               
[13] limma_3.42.2                GenomicFeatures_1.38.2      AnnotationDbi_1.48.0        Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[19] IRanges_2.20.2              S4Vectors_0.24.3            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] httr_1.4.2               bit64_0.9-7              assertthat_0.2.1         askpass_1.1              BiocFileCache_1.10.2     blob_1.2.1               GenomeInfoDbData_1.2.2  
 [8] Rsamtools_2.2.3          ggrepel_0.8.2            yaml_2.2.1               progress_1.2.2           pillar_1.6.1             RSQLite_2.2.0            lattice_0.20-40         
[15] glue_1.4.2               digest_0.6.27            XVector_0.26.0           colorspace_2.0-1         htmltools_0.5.1.1        Matrix_1.2-18            XML_3.99-0.3            
[22] pkgconfig_2.0.3          biomaRt_2.42.0           zlibbioc_1.32.0          purrr_0.3.4              scales_1.1.1             tibble_3.1.2             openssl_1.4.2           
[29] farver_2.0.3             generics_0.1.0           ellipsis_0.3.2           withr_2.4.2              cachem_1.0.5             cli_2.5.0                magrittr_2.0.1          
[36] crayon_1.4.1             memoise_2.0.0            evaluate_0.14            fansi_0.5.0              MASS_7.3-51.5            tools_3.6.2              prettyunits_1.1.1       
[43] hms_0.5.3                lifecycle_1.0.0          stringr_1.4.0            munsell_0.5.0            locfit_1.5-9.1           Biostrings_2.54.0        compiler_3.6.2          
[50] rlang_0.4.11             grid_3.6.2               RCurl_1.98-1.3           rstudioapi_0.13          rappdirs_0.3.1           labeling_0.4.2           bitops_1.0-6            
[57] rmarkdown_2.8            gtable_0.3.0             DBI_1.1.1                curl_4.3.1               R6_2.5.0                 GenomicAlignments_1.22.1 knitr_1.33              
[64] rtracklayer_1.46.0       fastmap_1.0.1            bit_4.0.4                utf8_1.1.4               stringi_1.6.2            Rcpp_1.0.6               vctrs_0.3.8             
[71] dbplyr_1.4.2             tidyselect_1.1.1         xfun_0.23
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