runEstimateStability: Command line execution for Stability

In HannahVMeyer/DrStable: Estimating the stability of dimensionality reduction results

Description

runEstimateStability runs without arguments. Upon call, it reads command-line parameters and supplies these to estimateStability. It reads the dimensionality reduction results from the cross-validation ( Rscript -e "Stability::runDimReduction()") and analyses the stability of the low-dimensional embedding via estimateStability. For details on estimateStability please refer to the help pages. The results of the analysis are written to 1) [output]/[method]_stability.csv which contains the stability estimate of the low-dimensional components for the specified [threshold] value and to 2) [output]/[method]_correlationCV.csv which contains the correlation of the low-dimensional components for all pairwise comparisons and components.

Usage

runEstimateStability()

Details

For help on the command line arguments that can be passed, see examples below. From the command line, the help function can be called via Rscript -e "Stability::runEstimateStability()" –args –help

Examples

# (not run)
# Rscript -e "Stability::runEstimateStability()" \
#--args \
#--highdim=/path/to/highdimfile \
#--cov=/path/to/optional/covariatefile \
#--seed=234 \
#--nrCV=10 \
#--neighbours=8 \
#--method=DRR \
#--name=Dimreduction_highdimfile \
#--outdir=/tmp \
#--showProgress \

HannahVMeyer/DrStable documentation built on Jan. 29, 2021, 11:42 a.m.