dot-loadingCor: Validating new dataset

In shbrief/PCAGenomicSignatures: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

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 human gene symbol format (HGNC). If dataset is a matrix, genes should be in rows and samples in columns. RNA-seq counts should be log(count + 1) prior to the 'validate()' call.
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, rows will be converted to z-score prior to PCA.

Value

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

shbrief/PCAGenomicSignatures documentation built on May 3, 2023, 11:21 a.m.