Frequently Asked Questions

library(TSAR)

FAQ

Verify Data Input

TSAR package processes large amounts of data of similar properties, it is easy to confuse one with another and fail analysis. Verify your data input and out here by check for variable names. Consider renaming your data frame to theese following if issues are encountered.

For more detailed examples, refers to vignettes, TSAR_Package_Structure and TSAR_Workflow_by_Command.

Locating Appropriate Function Calls

Given the two available workflows, here is a list of corresponding shiny functions and relative command line functions.

Under Data Pre-Processing, weed_raw():

Under Data Analysis, analyze_norm():

Under Data Visualization, graph_tsar():

Session Info

sessionInfo()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              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       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] TSAR_1.0.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] gtable_0.3.4        xfun_0.40           bslib_0.5.1        
#>  [4] ggplot2_3.4.4       shinyjs_2.1.0       htmlwidgets_1.6.2  
#>  [7] rstatix_0.7.2       lattice_0.22-5      vctrs_0.6.4        
#> [10] tools_4.3.1         generics_0.1.3      tibble_3.2.1       
#> [13] fansi_1.0.5         pkgconfig_2.0.3     Matrix_1.6-1.1     
#> [16] data.table_1.14.8   readxl_1.4.3        lifecycle_1.0.3    
#> [19] stringr_1.5.0       compiler_4.3.1      munsell_0.5.0      
#> [22] minpack.lm_1.2-4    carData_3.0-5       httpuv_1.6.12      
#> [25] shinyWidgets_0.8.0  htmltools_0.5.6.1   sass_0.4.7         
#> [28] yaml_2.3.7          lazyeval_0.2.2      plotly_4.10.3      
#> [31] later_1.3.1         pillar_1.9.0        car_3.1-2          
#> [34] ggpubr_0.6.0        jquerylib_0.1.4     tidyr_1.3.0        
#> [37] ellipsis_0.3.2      cachem_1.0.8        abind_1.4-5        
#> [40] nlme_3.1-163        mime_0.12           tidyselect_1.2.0   
#> [43] zip_2.3.0           digest_0.6.33       stringi_1.7.12     
#> [46] dplyr_1.1.3         purrr_1.0.2         splines_4.3.1      
#> [49] fastmap_1.1.1       grid_4.3.1          colorspace_2.1-0   
#> [52] cli_3.6.1           magrittr_2.0.3      utf8_1.2.4         
#> [55] broom_1.0.5         scales_1.2.1        promises_1.2.1     
#> [58] backports_1.4.1     rmarkdown_2.25      httr_1.4.7         
#> [61] ggsignif_0.6.4      cellranger_1.1.0    openxlsx_4.2.5.2   
#> [64] shiny_1.7.5.1       evaluate_0.22       knitr_1.44         
#> [67] viridisLite_0.4.2   mgcv_1.9-0          rlang_1.1.1        
#> [70] Rcpp_1.0.11         xtable_1.8-4        glue_1.6.2         
#> [73] rhandsontable_0.3.8 jsonlite_1.8.7      R6_2.5.1