How to run MOSAIC

Arshi Arora1

Source: vignettes/howtorun_MOSAIC.Rmd

In this package we provide the following datasets:

  1. cv.stats: This .Rdata object is the output of MOSAIC after running it for 50 rounds of 5-fold cross validation for all 13 - RNA data, 6 DNA Methylation and 6 DNA Accessibility data types.

  2. solnk: .Rdata object summarizing the cross validated solution for each data type, picked after comparing their Adjusted Mutual Information (AMI) and Standardized Pooled Within Sum of Squares (SPWSS) with the outcome of interest.

For scNMT seq data, MOSAIC was run as follows:

bigK = 7
library(doParallel)
registerDoParallel(cores=bigK)

library(MOSAIC)

load("stage.rmVisceralEnd.Rdata")
load("rna.mat.Rdata")

mat<-list(); mat[[1]] =x[names(stage),]

cvrounds<-function(x,out,kk){
    this.fold=5
    fit<-list()
    for (i in 1:50){
        fit[[i]] = cv.mosaic(x, out,kk,this.fold)

    }
    print(paste0("finished ", this.fold, " rounds for k= ", kk))
    return(fit)
}

cv.fit<-foreach(kk=2:bigK) %dopar% cvrounds(mat,stage,kk)

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