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.

### 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)