trainCS: Wrapper to train compression matrix

In bhattacharya-a-bt/DeCompress: Tissue compartment deconvolution for targeted RNA panels

Description

The function runs trainCS_gene over the entire set of genes needed for deconvolution from the reference dataset.

Usage

trainCS(
  yref,
  yref_need,
  seed = 1218,
  method = c("lar", "lasso", "enet", "ridge", "l1", "TV", "l2"),
  par = T,
  n.cores,
  lambda = 0.1
)

Arguments

yref	matrix, numeric expression matrix for target genes
yref_need	matrix, numeric expression matrix of needed genes
seed	numeric, random seed
method	vector, character vector of optimization methods
par	logical, T/F for parallelization
n.cores	numeric, number of cores
lambda	numeric, penalty paramemter for non-linear optimization

Value

list with coefficients and predictive R2

bhattacharya-a-bt/DeCompress documentation built on March 28, 2021, 3:52 a.m.