optimizeGFRN: Optimize GFRN gene lists lengths

In compbiomed/ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

Optimize GFRN gene lists lengths

Description

This function runs ASSIGN pathway prediction on gene list lengths from 5 to 500 to find the optimum gene list length for the GFRN pathways by correlating the ASSIGN predictions to a matrix of correlation data that you provide. This function takes a long time to run because you are running ASSIGN many times on many pathways, so I recommend parallelizing by pathway or running the ASSIGN predictions first (long and parallelizable) and then running the correlation step (quick) separately.

Usage

optimizeGFRN(
  indata,
  correlation,
  correlationList,
  run = c("akt", "bad", "egfr", "her2", "igf1r", "krasgv", "krasqh", "raf"),
  run_ASSIGN_only = FALSE,
  correlation_only = FALSE,
  keep_optimized_only = FALSE,
  pathway_lengths = c(seq(5, 20, 5), seq(25, 275, 25), seq(300, 500, 50)),
  iter = 1e+05,
  burn_in = 50000
)

Arguments

indata	The list of data frames from ComBat.step2
correlation	A matrix of data to correlate ASSIGN predictions to. The number of rows should be the same and in the same order as indata
correlationList	A list that shows which columns of correlation should be used for each pathway. See below for more details
run	specifies the pathways to predict. The default list will cause all eight pathways to be run in serial. Specify a pathway ("akt", "bad", "egfr", etc.) or list of pathways to run those pathways only.
run_ASSIGN_only	a logical value indicating if you want to run the ASSIGN predictions only. Use this to parallelize ASSIGN runs across a compute cluster or across compute threads
correlation_only	a logical value indicating if you want to run the correlation step only. The function will find the ASSIGN runs in the cwd and optimize them based on the correlation data matrix.
keep_optimized_only	a logical value indicating if you want to keep all of the ASSIGN run results, or only the runs that provided the optimum ASSIGN correlations. This will delete all directories in the current working directory that match the pattern "_gene_list". The default is FALSE
pathway_lengths	The gene list lengths that should be run. The default is the 20 pathway lengths that were used in the paper, but this list can be customized to which pathway lengths you are willing to accept
iter	The number of iterations in the MCMC.
burn_in	The number of burn-in iterations. These iterations are discarded when computing the posterior means of the model parameters.

Value

ASSIGN runs are output to the current workingdirectory. This function returns the correlation data and the optimized gene lists that you can use with runassignGFRN to try these lists on other data.

Examples

## Not run: 
testData <- read.table(paste0("https://drive.google.com/uc?authuser=0",
                              "&id=1mJICN4z_aCeh4JuPzNfm8GR_lkJOhWFr",
                              "&export=download"),
                       sep='\t', row.names=1, header=1)
corData <- read.table(paste0("https://drive.google.com/uc?authuser=0",
                             "&id=1MDWVP2jBsAAcMNcNFKE74vYl-orpo7WH",
                             "&export=download"),
                      sep='\t', row.names=1, header=1)
corData$negAkt <- -1 * corData$Akt
corData$negPDK1 <- -1 * corData$PDK1
corData$negPDK1p241 <- -1 * corData$PDK1p241

corList <- list(akt=c("Akt","PDK1","PDK1p241"),
                bad=c("negAkt","negPDK1","negPDK1p241"),
                egfr=c("EGFR","EGFRp1068"),
                her2=c("HER2","HER2p1248"),
                igf1r=c("IGFR1","PDK1","PDK1p241"),
                krasgv=c("EGFR","EGFRp1068"),
                krasqh=c("EGFR","EGFRp1068"),
                raf=c("MEK1","PKCalphap657","PKCalpha"))

combat.data <- ComBat.step2(testData, pcaPlots = TRUE)

optimization_results <- optimizeGFRN(combat.data, corData, corList)

## End(Not run)

compbiomed/ASSIGN documentation built on June 28, 2023, 4 a.m.