Updated HVTN065 script to use OpenCyto instead of the HIMCLyoplate code.
Added the option to run pipeline in parallel.
Updated the HVTN065 pipeline to reflect the latest changes to OpenCyto.
Updated HVTN065 pipeline to incorporate prior elicitation within stimulation groups. No longer do we need to create a GatingSet for each stimulation group.
Updated the HVTN065 pipeline to the new, more succinct way of group elicitation of priors.
Updated HVTN065 results summary after a successful pipeline run.
Added scripts to run pipeline and analyze results for several cytokine-quantile combinations.
Added initial code to calculate classification accuracies by cytokine-quantile combination with a pairing of patients.
Cleaned markers and simplified paired classification summary.
Initial move from the Sweave-like document to knitr:::spin. This is much nicer for a quick summary of the analysis that is independent of LaTeX.
Removed proportions summary.
Converted the Makefile to construct an HTML report via knitr:::spin.
Updated xtable results for HTML output. Also, returned additional information from the classification summary to construct ROC curves.
The gregmisc:::permutations function is deprecated and has been moved to the 'gtools' package. Changed code to reflect this.
Completed the first draft of the HVTN065 results report.
Cleaned up figures and updated probability thresholds to be nonnegative.
Fixed an issue in the ordering of the top quantiles. Should resolve incorrect reporting downstream.
The ordering of the results was being changed by 'plyr'. I resolved it by using mclapply instead.
Reporting the top 6 combos rather than the top 3.
Calculates AUCs by cytokine-quantile combination. Still need to rank AUCs, select markers, and plot ROCs for say, top 3, AUCs per stimulation.