collapseRowsUsingKME: Selects one representative row per group based on kME

Description

This function selects only the most informative probe for each gene in a kME table, only keeping the probe which has the highest kME with respect to any module in the module membership matrix. This function is a special case of the function collapseRows.

Usage

collapseRowsUsingKME(MM, Gin, Pin = NULL, kMEcols = 1:dim(MM)[2])

Value

datETcollapsed: A numeric matrix with the same columns as the input matrix MM, but with rows corresponding to the genes rather than the probes.
group2row: A matrix whose rows correspond to the unique gene labels and whose 2 columns report which gene label (first column called group) is represented by what probe (second column called selectedRowID)
selectedRow: A logical vector whose components are TRUE for probes selected as representatives and FALSE otherwise. It has the same length as the vector Pin.

Arguments

MM: A module membership (kME) table with at least a subset of the columns corresponding to kME values.
Gin: Genes labels in a 1 to 1 correspondence with the rows of MM.
Pin: If NULL (default), rownames of MM are assumed to be probe IDs. If entered, Pin must be the same length as Gin and correspond to probe IDs for MM.
kMEcols: A numeric vector showing which columns in MM correspond to kME values. The default is all of them.

Author

Jeremy Miller

Examples

Run this code

# Example: first simulate some data
set.seed(100)
ME.A = sample(1:100,50);  ME.B = sample(1:100,50)
ME.C = sample(1:100,50);  ME.D = sample(1:100,50)  
ME1     = data.frame(ME.A, ME.B, ME.C, ME.D)
simDatA = simulateDatExpr(ME1,1000,c(0.2,0.1,0.08,0.05,0.3), signed=TRUE)
simDatB = simulateDatExpr(ME1,1000,c(0.2,0.1,0.08,0.05,0.3), signed=TRUE)
Gin     = c(colnames(simDatA$datExpr),colnames(simDatB$datExpr))
Pin     = paste("Probe",1:length(Gin),sep=".")
datExpr = cbind(simDatA$datExpr, simDatB$datExpr)
MM      = corAndPvalue(datExpr,ME1)$cor

# Now run the function and see some example output
results = collapseRowsUsingKME(MM, Gin, Pin)
head(results$MMcollapsed)
head(results$group2Row)
head(results$selectedRow)