Allow pluggable similarity measure to validate.

[seandavi]

• Spearman
• other methods from dist
• straight function

GenomicSuperSignature/R/validate.R

Lines 15 to 37 in 5e73d06

	.loadingCor <- function(dataset, avgLoading, method = "pearson", scale = FALSE) {
	if (any(class(dataset) == "ExpressionSet")) {
	dat <- Biobase::exprs(dataset)
	} else if (any(class(dataset) %in% c("SummarizedExperiment", "RangedSummarizedExperiment"))) {
	dat <- SummarizedExperiment::assay(dataset)
	} else if (any(class(dataset) == "matrix")) {
	dat <- dataset
	} else {
	stop("'dataset' should be one of the following objects: ExpressionSet,
	SummarizedExperiment, RangedSummarizedExperiment, and matrix.")
	}
	if (isTRUE(scale)) {dat <- rowNorm(dat)} # row normalization
	dat <- dat[apply(dat, 1, function (x) {!any(is.na(x) | (x==Inf) | (x==-Inf))}),]
	gene_common <- intersect(rownames(avgLoading), rownames(dat))
	prcomRes <- stats::prcomp(t(dat[gene_common,])) # centered, but not scaled by default
	loadings <- prcomRes$rotation[, 1:8]
	loading_cor <- abs(stats::cor(avgLoading[gene_common,], loadings[gene_common,],
	use = "pairwise.complete.obs",
	method = method))
	return(loading_cor)
	}