runDimensionalityReduction: Command line execution for Dimensionality reduction

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

Description

runDimensionalityReduction runs without arguments. Upon call, it reads command-line parameters and reads the [highdim] and potential [cov] data. If provided, [cov] will be regressed from [highdim] prior to dimensionality reduction. Dimensionality reduction and saving of the results are done by passing the [highdim] data, [method], [dim], [neighbours] and potential optional other, method-specific parameters ([dimRedParams]) to computeDimReduction and saveDimReduction. For details on input to computeDimReduction and saveDimReduction, please refer to their help pages. 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::runDimensionalityReduction()" –args –help

Usage

runDimensionalityReduction()

Examples

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

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