Codes to reproduce analysis from Dey and Stephens (2018+)

Here are the analysis RmD files for reproducing the figures from our paper. To run these scripts, first clone the source directory

git clone https://github.com/kkdey/CorShrink-pages.git

Then go to the analysis directory

cd CorShrink-pages/analysis

The paths of the data files in the scripts below (under Figures and Supplementary Figures) are relative to this directory.

Figures :

• Figure 1: CorShrink on PLIN1 gene expression data

• Figure 2: CorShrink on expression data from other genes

• Figure 3: FLASH and softImpute imputation on PLIN1 gene expression

• Figure 4: Correlation Matrix Distance (CMD) comparison of CorShrink with other methods on different simulation designs

• Figure 5: Eigenvalue trends comparison of CorShrink with other methods on different simulation designs

• Figure 6: Corshrink on word2vec similarity estimates from Ebony magazine 1968 issues

Supplementary Figures :

• Supplementary Figure 1: CorShrink with different shrinkage priors

• Supplementary Figure 2: Tissue pair and gene-based CorShrink

• Supplementary Figure 3: Frobenius distance comparison of CorShrink with other methods on different simulation designs

• Supplementary Figure 4: Frobenius distance comparison of pCorShrink, CLIME, ISEE and GLASSO

• Supplementary Figure 5: Frobenius distance comparison of partial correlations from CorShrink and other methods on different simulation designs

• Simulation comparson of FLASH and CorShrink with missing data

Additional analyses