README.Rmd

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output: github_document
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# PhaseX.2 Quality Control R package

The goal of PhaseX.2QCpackage is to perform Quality Control on data generated for 4CE phase 1.2 and  phase 2.2.



## Installing the package and running QC

This version of the package should NOT be run on Docker. Please run the following script to load the package and run QC.

```{r, eval=FALSE}
### install the package
devtools::install_github("https://github.com/covidclinical/PhaseX.2QualityControlRpackage", upgrade=FALSE)
library(PhaseX.2QualityControlRpackage)

### enter input path, output path and site name
dir.input1.2 = ""       # path that contains phase 1.2 data
dir.input2.2 = ""       # path that contains phase 2.2 data, write NA if 2.2 data is not available
dir.output = ""         # path to save the QC reports
select.all.cohorts = F  # equal F to display the report for a subset of cohorts
site.nm = ""            # 4CE site ID

### run QC
runQC(dir.input1.2, dir.input2.2, dir.output, select.all.cohorts=F, site.nm)
```