Introduction

Gene expression measurements can be summarized into a signature or set of genes to create a score that represents the activity of that set of genes in a sample. By summarizing genes in known signaling pathways, cells with active signaling pathways or specific cellular functions can be identified. Gene Set Variation Analysis (GSVA) uses gene sets to create these signatures.

Manual Input

The SCTK can profile pathway activity using signatures saved in the gene annotation data frames in a SCtkExperiment object. These pathway annotations should be numeric vectors of 1 (in signature) and 0 (not in signature).

MSigDB

For human samples with entrez gene id annotations, it is possible to perform pathway activity analysis across MSigDB c2 or a subset of MSigDB. Choose a condition and the pathway tab will report the top differentially active pathways across that annotation.

Visualization

Pathway activity results can be visualized in the “Plot” tab using either a heatmap or a violin plot. A condition variable is required for the violin plots.

Save Pathway Results

Pathway results can be saved in the SCTK gene annotation data frame or downloaded directly in the pathway activity tab.

Session info

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.4
## 
## 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] stats     graphics  grDevices utils     datasets  methods   base     
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## other attached packages:
## [1] BiocStyle_2.12.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.1         rstudioapi_0.10    knitr_1.22        
##  [4] xml2_1.2.0         magrittr_1.5       roxygen2_6.1.1    
##  [7] MASS_7.3-51.4      R6_2.4.0           rlang_0.3.4       
## [10] stringr_1.4.0      tools_3.6.0        xfun_0.6          
## [13] htmltools_0.3.6    commonmark_1.7     yaml_2.2.0        
## [16] digest_0.6.18      assertthat_0.2.1   rprojroot_1.3-2   
## [19] bookdown_0.9       pkgdown_1.3.0      crayon_1.3.4      
## [22] BiocManager_1.30.4 fs_1.3.0           memoise_1.1.0     
## [25] evaluate_0.13      rmarkdown_1.12     stringi_1.4.3     
## [28] compiler_3.6.0     desc_1.2.0         backports_1.1.4