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erccdashboard-shiny-app

Shiny app for the erccdashboard R package

This Shiny app utilizes the R erccdashboard package to assess technical performance of gene expression experimetns when using the ERCC controls. This app displays the output of the erccdashboard package and allows for some plot interactions to evaluate individual or mulitple data points.

To run the app you will need to bring the following in to an R Studio session: DESCRIPTION, ui.R, server.R

Below is the R Studio session information under which the application was developed:

R version 3.2.1 (2015-06-18) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite)

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
[5] datasets methods base

other attached packages: [1] erccdashboard_1.6.0 gridExtra_2.2.1
[3] ggplot2_2.1.0 DT_0.2
[5] shiny_0.14

loaded via a namespace (and not attached): [1] Rcpp_0.12.7 pracma_1.9.5
[3] plyr_1.8.4 bitops_1.0-6
[5] tools_3.2.1 digest_0.6.10
[7] jsonlite_1.1 gtable_0.2.0
[9] nlme_3.1-128 lattice_0.20-34
[11] mgcv_1.8-15 Matrix_1.2-7.1
[13] yaml_2.1.13 QuasiSeq_1.0-8
[15] stringr_1.1.0 sourcetools_0.1.5 [17] htmlwidgets_0.7 gtools_3.5.0
[19] caTools_1.17.1 locfit_1.5-9.1
[21] grid_3.2.1 qvalue_2.2.2
[23] R6_2.1.3 limma_3.26.9
[25] gdata_2.17.0 reshape2_1.4.1
[27] ROCR_1.0-7 edgeR_3.12.1
[29] magrittr_1.5 splines_3.2.1
[31] scales_0.4.0 gplots_3.0.1
[33] htmltools_0.3.5 MASS_7.3-45
[35] mime_0.5 xtable_1.8-2
[37] colorspace_1.2-6 httpuv_1.3.3
[39] labeling_0.3 quadprog_1.5-5
[41] KernSmooth_2.23-15 stringi_1.1.1
[43] munsell_0.4.3

Current Limitations of app

There are currently some limitations of the app that will hopefully be rectified upon updates to the erccdashboard package code. Currently only the Dynamic Range and MA plots are interactive. To obtain the console output click on the "Console Output" tab. In the current version runDashboard() is called a second time to display the console output within the app. This is not ideal or efficient. Further updates to this will occur when the dashboard code is updated.

Run with test data set

If you run the app using the supplied MET.CTL.countDat.csv dataset, load the data set use the browse button within the app. Once the dataset is displayed adjust "Sample 1 Name" and "Sample 2 Name" to be "MET" and "CTL", respectively. Enter a prefix for output file name. All other fields are default values and appropriate for this dataset however these values can be overridden with user input. Once all information is entered click the "Run!" button. The "Run!" button tells the server all information is up to date and is ready to execute. When the "erccdashboard Plots" tab is clicked the runDashboard() will be executed and the tab will take a couple of minutes to populate with the plots. To display the output from the console click on the "Console Output" tab. This will execute runDashboard() and display the console output along with the list object generated by the dashboard. Again with this take a couple of minutes to populate.

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Shiny app for the erccdashboard R package

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