.loadingCor {GenomicSuperSignature}R Documentation

Validating new dataset

Description

Validating new dataset

Usage

.loadingCor(dataset, avgLoading, method = "pearson", scale = FALSE)

Arguments

dataset

A gene expression profile to be validated. Different classes of objects can be used including ExpressionSet, SummarizedExperiment, RangedSummarizedExperiment, or matrix. Rownames (genes) should be in symbol format. If it is a matrix, genes should be in rows and samples in columns.

avgLoading

A matrix with genes by RAVs.

method

A character string indicating which correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman": can be abbreviated.

scale

Default is FALSE. If it is set to TRUE, dataset will be row normalized by rowNorm function.

Value

A matrix of Pearson correlation coefficient (default, defined through method argument) between RAVs (row) and the top 8 PCs from the datasets (column)


[Package GenomicSuperSignature version 1.1.8 Index]