Create new tests

[dimalvovs]

The tests present in the /tests/ seem outdated: those refer to code that does not exist (example - CoParams), to old testing data that was removed (example data/GSE98638_HCC.TCell.S5063.count.txt), as well as lack the structure. Tests need to rewritten.

[dimalvovs]

• modSim default parameters test
• distributed parameters run test
• useful tests from existing suit
• github workflow for auto-testing

[dimalvovs]

one problem with comparing the results on same dataset at different times (seeds) is that the ordering of rows in the resulting matrices may change. attaching a historic script used to reorder the matrices for future comparison.

# reorderByPatternMatch: function to identify corresponding rows
#                        between two P matrices
# History: EJF - original CoGAPS

# Inputs: P - matrix to be matched
#         matchTo - matrix to match P to

# Output: P with reordered rows to match matchTo

#'\code{reorderByPatternMatch} plots the output A and P matrices as a
#' heatmap and line plot respectively
#'
#'@param P matrix to be matched
#'@param matchto matrix to match P to
#'@export

reorderByPatternMatch <- function(P, matchTo) {
	
	# check that P and the matchTo matrix have the same dimensions for valid matching
	if (nrow(matchTo) != nrow(P) | ncol(matchTo) != ncol(P)) {
		stop('CoGAPS: reorderByPatternMatch: dimensions of P and matchTo must agree')
	}
	
	# ensuring that rownames match for simplicty of matching process
	row.names(matchTo) <- row.names(P)
	
	# compute the correlation between each entry
	corP <- cor(t(matchTo),t(P))
	
	# initalize the new matrix
	pMatch <- rep(0, nrow(P))
	names(pMatch) <- row.names(P)
	
	# match patterns in order of correlation
	for (p in 1:(nrow(P)-1)) {
		ptemp <- which(corP==max(corP),arr.ind=T)
		pMatch[row.names(corP)[ptemp[1]]] <- colnames(corP)[ptemp[2]]
		if (length(corP) > 1) {
			corP <- corP[-ptemp[1],-ptemp[2]]
		}
    }
    pMatch[which(pMatch==0)] <- setdiff(names(pMatch), pMatch)
	
	# return matched patterns
	return(P[pMatch,])
	
}