knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
This vignette first describes each of the raw data files. It then provides a diagram outlining how the data preparation R scripts are run to prepare the raw data for analysis, as well as the resultant outputs.
The raw data provided are not cell counts, but are the frequencies of cells producing some combination of the cytokines IFN$\gamma$, IL-2 and TNF. All raw data except that in the file megapool.csv also include IL-17, and the file bcg.xlsx also included IL-22.
There are two files associated with H1. They are detailed separately below. THe first, h1-group_info.xlsx, was used to determine which study group each participant was allocated to, where the group determines the dose size and number of doses. The second, h1.xlsx, contains the immune response measurements.
Columns
File name
To automatically load and format the raw data into the tables used for analysis, there are two steps:
No further actions should be necessary, as Makefile.R will automatically find where the spreadsheets are located and run the formatting files in the correct order. The global environment will then contain all the tables used in the analysis (and some others), which are detailed below.
The schematic describes data processing by stage, specifying the outputs and processing files and providing details.
knitr::include_graphics("Data_Prep_Flow.png")
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