Allow configurable number of PCs in validate

[seandavi]

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)
	}

[shbrief]

1. Add the option of how many PCs you can compare with RAVs for validation
2. Add 'scree plot' of new data as an additional guidance (in addition to scores and avg.silhouette.width)