Last updated: 2020-09-25

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Knit directory: single-cell-topics/analysis/

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Here we perform a differential expression analysis using the topic model fit to the droplet data.

Load the packages used in the analysis below.

library(Matrix)
library(dplyr)
library(fastTopics)
library(tools)

Load data and results

Load the droplet data.

load("../data/droplet.RData")

Load the \(k = 7\) Poisson NMF model fit.

fit <- readRDS("../output/droplet/rds/fit-droplet-scd-ex-k=7.rds")$fit

Load the clusters identified in the clustering analysis.

samples <- readRDS("../output/droplet/clustering-droplet.rds")

Perform differential expression analysis

Perform differential expression analysis using the multinomial topic model.

timing <- system.time(
  diff_count_topics <- diff_count_analysis(fit,counts))
cat(sprintf("Computation took %0.2f seconds.\n",timing["elapsed"]))
# Fitting 18388 x 7 = 128716 univariate Poisson models.
# Computing log-fold change statistics.
# Computation took 23.76 seconds.

Next, calculate differential expression statistics using the clusters that were identified from the topic proportion PCs.

fit_clusters <- init_poisson_nmf_from_clustering(counts,samples$cluster)
timing <- system.time(
  diff_count_clusters <- diff_count_analysis(fit_clusters,counts))
# All topic proportions are either zero or one; using simpler single-topic calculations for model parameter estimates
cat(sprintf("Computation took %0.2f seconds.\n",timing["elapsed"]))
# Fitting 18388 x 8 = 147104 univariate Poisson models.
# Computing log-fold change statistics.
# Computation took 25.88 seconds.

Finally, perform one more differential expression analysis after first merging the two topics for club cells.

fit_merge_club <- merge_topics(poisson2multinom(fit),c(5,7))
timing <- system.time(
  diff_count_merge_club <- diff_count_analysis(fit_merge_club,counts))
cat(sprintf("Computation took %0.2f seconds.\n",timing["elapsed"]))
# Fitting 18388 x 6 = 110328 univariate Poisson models.
# Computing log-fold change statistics.
# Computation took 17.14 seconds.

Save results

Save the results of the differential expression analyses to an RData file.

save(list = c("diff_count_topics",
              "diff_count_clusters",
              "diff_count_merge_club"),
     file = "diff-count-droplet.RData")
resaveRdaFiles("diff-count-droplet.RData")

sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.6
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.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] tools     stats     graphics  grDevices utils     datasets  methods  
# [8] base     
# 
# other attached packages:
# [1] fastTopics_0.3-177 dplyr_0.8.3        Matrix_1.2-18     
# 
# loaded via a namespace (and not attached):
#  [1] progress_1.2.2       tidyselect_0.2.5     xfun_0.11           
#  [4] purrr_0.3.3          lattice_0.20-38      vctrs_0.2.1         
#  [7] colorspace_1.4-1     viridisLite_0.3.0    htmltools_0.4.0     
# [10] yaml_2.2.0           MCMCpack_1.4-5       plotly_4.9.2        
# [13] rlang_0.4.5          later_1.0.0          pillar_1.4.3        
# [16] glue_1.3.1           lifecycle_0.1.0      stringr_1.4.0       
# [19] MatrixModels_0.4-1   munsell_0.5.0        gtable_0.3.0        
# [22] workflowr_1.6.2.9000 htmlwidgets_1.5.1    coda_0.19-3         
# [25] evaluate_0.14        knitr_1.26           SparseM_1.78        
# [28] httpuv_1.5.2         quantreg_5.54        irlba_2.3.3         
# [31] Rcpp_1.0.5           promises_1.1.0       backports_1.1.5     
# [34] scales_1.1.0         jsonlite_1.6         RcppParallel_4.4.2  
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# [55] whisker_0.4          pkgconfig_2.0.3      MASS_7.3-51.4       
# [58] prettyunits_1.1.1    data.table_1.12.8    assertthat_0.2.1    
# [61] rmarkdown_2.3        httr_1.4.1           R6_2.4.1            
# [64] git2r_0.26.1         compiler_3.6.2