optimize_parameters: Constructing robust reference standards for Nof1 studies for...

In SamirRachidZaim/referenceNof1: ‘Develops Robust Nof1 Reference Standards for Single-Subject Studies in Precision Medicine’

Description

referenceNof1 is the R implementation of the reference biomarker algorithm by (Zaim 2020)

Usage

optimize_parameters(gs.mat=utils::data("mcf7"),
                           expressionCutoffs = c(30,50),
                           FCRegions = list(c(0,0.3)),
                           FDR.cutoff = 0.1)

Arguments

gs.mat	the matrix used to develop the reference standard
expressionCutoffs	a vector of positive integer > 1 indicating the minimum count value of RNA-seq
FCCutoff	a list of upper bounds for minimal fold change thresholds
FDR.cutoff	fdr.threshold for determining which set of genes are DEGs in the reference standard
targetJI	target jaccard index

SamirRachidZaim/referenceNof1 documentation built on Oct. 24, 2020, 2:22 p.m.