Contents

1 Summary of the output objects of scTensor

Here, we introduced the objects saved in reanalysis.RData.

suppressPackageStartupMessages(library("scTensor"))
load("reanalysis.RData")

After performing cellCellReport, some R objects are saved in the reanalysis.RData as follows;

2 Execution of scTensor with the different options

Using the reanalysis.RData, some user may want to perform scTensor with different parameters.

For example, the user can perform cellCellDecomp with different ranks, and also can peform cellCellReport with omiting some enrichment analysis step as follows.

suppressPackageStartupMessages(library("LRBase.Hsa.eg.db"))
# Register the file pass of user's LRBase
metadata(sce)$lrbase <- dbfile(LRBase.Hsa.eg.db)
# CCI Tensor Decomposition
cellCellDecomp(sce, ranks=c(6,5), assayNames="normcounts")
# HTML Report
cellCellReport(sce, reducedDimNames="TSNE", assayNames="normcounts",
    title="Cell-cell interaction within Germline_Male, GSE86146",
    author="Koki Tsuyuzaki", html.open=TRUE,
    goenrich=TRUE, meshenrich=FALSE, reactomeenrich=FALSE,
    doenrich=FALSE, ncgenrich=FALSE, dgnenrich=FALSE)

Session information

## R Under development (unstable) (2019-10-24 r77329)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.11-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] AnnotationHub_2.19.1                   
##  [2] BiocFileCache_1.11.2                   
##  [3] dbplyr_1.4.2                           
##  [4] Homo.sapiens_1.3.1                     
##  [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [6] org.Hs.eg.db_3.10.0                    
##  [7] GO.db_3.10.0                           
##  [8] OrganismDbi_1.29.0                     
##  [9] GenomicFeatures_1.39.0                 
## [10] AnnotationDbi_1.49.0                   
## [11] MeSH.Mmu.eg.db_1.13.0                  
## [12] LRBase.Mmu.eg.db_1.2.0                 
## [13] MeSH.Hsa.eg.db_1.13.0                  
## [14] MeSHDbi_1.23.0                         
## [15] SingleCellExperiment_1.9.0             
## [16] SummarizedExperiment_1.17.0            
## [17] DelayedArray_0.13.0                    
## [18] BiocParallel_1.21.0                    
## [19] matrixStats_0.55.0                     
## [20] Biobase_2.47.0                         
## [21] GenomicRanges_1.39.1                   
## [22] GenomeInfoDb_1.23.0                    
## [23] IRanges_2.21.1                         
## [24] S4Vectors_0.25.0                       
## [25] BiocGenerics_0.33.0                    
## [26] scTensor_1.3.1                         
## [27] RSQLite_2.1.2                          
## [28] LRBase.Hsa.eg.db_1.2.0                 
## [29] LRBaseDbi_1.5.0                        
## [30] BiocStyle_2.15.0                       
## 
## loaded via a namespace (and not attached):
##   [1] rappdirs_0.3.1                rtracklayer_1.47.0           
##   [3] AnnotationForge_1.29.1        tidyr_1.0.0                  
##   [5] ggplot2_3.2.1                 acepack_1.4.1                
##   [7] bit64_0.9-7                   knitr_1.25                   
##   [9] data.table_1.12.6             rpart_4.1-15                 
##  [11] RCurl_1.95-4.12               AnnotationFilter_1.11.0      
##  [13] cowplot_1.0.0                 europepmc_0.3                
##  [15] bit_1.1-14                    enrichplot_1.7.0             
##  [17] webshot_0.5.1                 xml2_1.2.2                   
##  [19] httpuv_1.5.2                  assertthat_0.2.1             
##  [21] viridis_0.5.1                 xfun_0.10                    
##  [23] hms_0.5.2                     evaluate_0.14                
##  [25] promises_1.1.0                TSP_1.1-7                    
##  [27] progress_1.2.2                caTools_1.17.1.2             
##  [29] dendextend_1.12.0             Rgraphviz_2.31.0             
##  [31] igraph_1.2.4.1                DBI_1.0.0                    
##  [33] htmlwidgets_1.5.1             MeSH.db_1.13.0               
##  [35] purrr_0.3.3                   dplyr_0.8.3                  
##  [37] backports_1.1.5               bookdown_0.14                
##  [39] annotate_1.65.0               biomaRt_2.43.0               
##  [41] vctrs_0.2.0                   ensembldb_2.11.0             
##  [43] abind_1.4-5                   ggforce_0.3.1                
##  [45] Gviz_1.31.0                   triebeard_0.3.0              
##  [47] BSgenome_1.55.0               checkmate_1.9.4              
##  [49] GenomicAlignments_1.23.0      gclus_1.3.2                  
##  [51] fdrtool_1.2.15                prettyunits_1.0.2            
##  [53] cluster_2.1.0                 DOSE_3.13.0                  
##  [55] dotCall64_1.0-0               lazyeval_0.2.2               
##  [57] crayon_1.3.4                  genefilter_1.69.0            
##  [59] pkgconfig_2.0.3               tweenr_1.0.1                 
##  [61] ProtGenerics_1.19.0           seriation_1.2-8              
##  [63] nnet_7.3-12                   rlang_0.4.1                  
##  [65] lifecycle_0.1.0               meshr_1.23.0                 
##  [67] registry_0.5-1                MeSH.PCR.db_1.13.0           
##  [69] rTensor_1.4                   GOstats_2.53.0               
##  [71] dichromat_2.0-0               polyclip_1.10-0              
##  [73] graph_1.65.0                  Matrix_1.2-17                
##  [75] urltools_1.7.3                base64enc_0.1-3              
##  [77] ggridges_0.5.1                viridisLite_0.3.0            
##  [79] MeSH.AOR.db_1.13.0            bitops_1.0-6                 
##  [81] visNetwork_2.0.8              KernSmooth_2.23-16           
##  [83] spam_2.4-0                    MeSH.Bsu.168.eg.db_1.13.0    
##  [85] Biostrings_2.55.0             blob_1.2.0                   
##  [87] stringr_1.4.0                 qvalue_2.19.0                
##  [89] nnTensor_1.0.2                gridGraphics_0.4-1           
##  [91] reactome.db_1.70.0            scales_1.0.0                 
##  [93] graphite_1.33.0               memoise_1.1.0                
##  [95] GSEABase_1.49.0               magrittr_1.5                 
##  [97] plyr_1.8.4                    gplots_3.0.1.1               
##  [99] gdata_2.18.0                  zlibbioc_1.33.0              
## [101] compiler_4.0.0                RColorBrewer_1.1-2           
## [103] plotrix_3.7-6                 Rsamtools_2.3.2              
## [105] XVector_0.27.0                Category_2.53.1              
## [107] MeSH.Aca.eg.db_1.13.0         htmlTable_1.13.2             
## [109] Formula_1.2-3                 MASS_7.3-51.4                
## [111] tidyselect_0.2.5              stringi_1.4.3                
## [113] highr_0.8                     MeSH.Syn.eg.db_1.13.0        
## [115] yaml_2.2.0                    GOSemSim_2.13.0              
## [117] askpass_1.1                   latticeExtra_0.6-28          
## [119] ggrepel_0.8.1                 grid_4.0.0                   
## [121] VariantAnnotation_1.33.0      fastmatch_1.1-0              
## [123] tools_4.0.0                   rstudioapi_0.10              
## [125] foreach_1.4.7                 foreign_0.8-72               
## [127] tagcloud_0.6                  outliers_0.14                
## [129] gridExtra_2.3                 farver_1.1.0                 
## [131] ggraph_2.0.0                  rvcheck_0.1.6                
## [133] digest_0.6.22                 BiocManager_1.30.9           
## [135] shiny_1.4.0                   Rcpp_1.0.3                   
## [137] BiocVersion_3.11.0            later_1.0.0                  
## [139] httr_1.4.1                    cummeRbund_2.29.0            
## [141] biovizBase_1.35.0             colorspace_1.4-1             
## [143] XML_3.98-1.20                 splines_4.0.0                
## [145] fields_9.9                    RBGL_1.63.1                  
## [147] graphlayouts_0.5.0            ggplotify_0.0.4              
## [149] plotly_4.9.1                  xtable_1.8-4                 
## [151] jsonlite_1.6                  heatmaply_0.16.0             
## [153] tidygraph_1.1.2               zeallot_0.1.0                
## [155] R6_2.4.0                      Hmisc_4.3-0                  
## [157] pillar_1.4.2                  htmltools_0.4.0              
## [159] mime_0.7                      glue_1.3.1                   
## [161] fastmap_1.0.1                 interactiveDisplayBase_1.25.0
## [163] codetools_0.2-16              maps_3.3.0                   
## [165] fgsea_1.13.0                  lattice_0.20-38              
## [167] tibble_2.1.3                  curl_4.2                     
## [169] gtools_3.8.1                  ReactomePA_1.31.0            
## [171] misc3d_0.8-4                  openssl_1.4.1                
## [173] survival_3.1-7                rmarkdown_1.16               
## [175] munsell_0.5.0                 DO.db_2.9                    
## [177] GenomeInfoDbData_1.2.2        plot3D_1.1.1                 
## [179] iterators_1.0.12              reshape2_1.4.3               
## [181] gtable_0.3.0