QC pipeline

[shraddhapai]

We need a pipeline for preprocessing steps in assessing data quality and data cleaning before running the predictor. Currently there is no such mechanism in place. Operations pipeline would run:

• identify structure in missingness of data
• identify and flag outlier samples
• run some unsupervised analyses on the samples. e.g. pca, hierarchical clustering
• For continuous-valued data, compare several similarity metrics to find one which best separates classes. e.g. RNAcorr.R written by SP for PanCancer
• Hierarchical clustering of classes and PCA, following same idea.
• Running univariate test to prune matrix of variables that goes into netDx.